The issue is that all the Dataheets are reporting
1 = E
2 = B
3 = C
geometrically located as it is fromt he Datasheet.
Kicad has the same numbers but geometrically is inverted: B with C
Actually this is your mistake. The part you wanted to use was MMBT3904, as is said in the datasheet. 2N3904 is only the TO-92 version.
Open the footprint, and lo behold:
Well, to be honest, I have KiCad v7.99.
From your first post it looks that practically you are looking for MMBT3904.
I failed to find this transistor datasheet saying pins are: 123=EBC.
Diotec:123=BEC
https://www.mouser.pl/datasheet/2/849/mmbt3904-2577512.pdf
Taiwan Semicronductor: 123=BEC
https://www.mouser.pl/datasheet/2/395/MMBT3904_E2001-1918270.pdf
OnSemi: 123=BEC
https://www.mouser.pl/datasheet/2/308/MMBT3904LT1_D-1811574.pdf
Diodes: not uses numbers
Nexperia (NXP): 123=BEC
https://www.mouser.pl/datasheet/2/916/MMBT3904-1365817.pdf
Infineon: 123=BEC
https://www.mouser.pl/datasheet/2/196/Infineon-SMBT3904SERIES-DS-v01_01-en-1226678.pdf
MCC: not uses numbers
https://www.mouser.pl/datasheet/2/258/MMBT3904_SOT_23_-2510634.pdf
Piotr seems to have gone even further than I did. But it was enough to try to find a 2N3904 in Digikey and Mouser and some google images. They are all TO packages, so 2N3904 comes in that kind of package by definition and can’t have the SOT package. No wonder it went wrong when you changed the footprint.
If you (tormy) wonder how the same footprint you already tried can now be correct, it was exactly as was told: the symbol is different. The footprint has always the same pad numbers but in the view above shows dynamically the attached symbol’s pin names.
One valid finding from this “issue” is that MMBT3904 symbol in the official libraries, has a wrong datasheet. This will be fixed soon ( i am guessing here ).
Other than that, it is a working ( trouble free ) part based on this.
2N3904S is not in the official libraries, and its datasheet doesn’t seem to follow IPC numbering.
(Not that the ds i linked above does, but at least they didn’t have any confusing numbers in there…)
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Yes I hope the S version will be included.
However: it’s a very confusing situation this. A lot!
Now you’re showing datasheet for 2N3904S. It’s easy to admit you found one with SOT, but still it’s not MMBT3904 which was in your first datasheet and which is in the KiCad library – without error. 2N3904 is also correct in the library. There just isn’t a wrong symbol or footprint among these in the KiCad libraries.
You can’t just take one symbol or footprint pin numbering from a datasheet describing a specific part and apply it to another part.
This we agree on, although it’s not caused by KiCad. I hope everyone reading this thread will remember to double check the datasheets, symbols and footprints they are using. The situation with transistors is like that, whatever EDA or library you are using.
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That one is also wrong 'cause points the emitter to pin 2 while in the KEC is pin 1.
however now double check on all details even if they seem equal to each other
I am using 7.0.2 and when I type ‘2N3904’ into the filter at the add symbol box I get a single option and that is for a TO-92 package, nothing else and it is correct. If I type in ‘3904’ without the ‘2N’ then I get a list with 7 entries comprising of ‘2N3904’ and 6 others, when I highlight the ‘2N3904’ I am again shown a TO-92 package with pin 2 as the base and all is well, now if I move to the variant ‘MMBT3904’ I see a symbol with pin 1 as the base and a SOT-23 package so I go to a datasheet for the device at Mouser and find that pin 1 is indeed the base in this package again all is well. The only part of this that could possibly cause confusion is the fact that KICAD offers the same Datasheet address for both devices which I guess could catch out the young players. In summary ‘2N3904’ gives me 1 symbol and footprint which are correct and ‘3904’ gives me a choice of packages and I select ‘MMBT3904’ from the list and I get 1 symbol and a SMD SOT-23 footprint that is correct but I check this stuff again at layout time…just thought I would add to the confusion and give you my take on it 
Ever since I started to shift from metal TO-18 to plastic TO-92, more than 40 years ago, I have been occasionally caught out by erratic pin numbering between brands of what should have been the same device.
You learn to check and check again
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According to the Fairchild datasheet the symbol and the footprint are correct. You still seem to fail to understand that the KEC datasheet is for 2N3904S exclusively, not for MMBT3904. I said MMBT3904 in the KiCad libraries is correct, you say it’s wrong because 2N3904S datasheet has the pins in different order. Why do you insist mixing data from different parts? That was your original mistake which lead to a faulty board: you took a symbol for 2N3904 and attached a MMBT3904 compatible footprint to it. Why you suppose that 2N3904S footprint (which yet another different part!) and MMBT3904 footprint should be identical as for the pin order?
According to my understanding they are identical as for the pin order. Only at datasheet pin names are different, but it is only a paper.
In ‘>’ order the KiCad footprint is 1 3 2. The KEC footprint, shown in posts by tormyvancool, is 2 3 1. In Fairchild it’s 1 3 2.
EDIT: in both datasheets the functional order (read in the same way ‘>’) is B C E. But the number/name connections are different because the numbering order is different.
Yep indeed. By checking all the microdetails.
Yes this was the tricky part.
And (however we name footprint pads) it is the only one what should be understood as ‘pin order’ for bipolar transistor.
If KiCad SOT23 pads were named BOTTOM_LEFT, BOTTOM_RIGHT and TOP there would be less risk of such error, I think.
But I don’t postulate such change 
@Aris_Kimi in a long discussion I had privately an don GitLab with him, he made me read the IPC 7351 page 77 if I remember correctly.
On that document the pin 1 is upper left he 2 lower left.
Right?
Ok, if you get the KEC datasheet you can see that IT IS the SOT-23. But they inverted it.
It’s NOT question of the S or else.It’s question they didn’t respected the SOT-23.
So who’s right who’s wrong is hard to say.
I went back to the project and I rebuilt the history (it was schematised in Jan 2022).
Today I also recuperate the email with the chat with JLCPCB
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Yes I chosen for the MMBT version.
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When I went on JLCPCB THAT MMBT was not available (shortage) at THAT time.
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I asked to JLCPCB in chat and they answered that the component was not available due semiconductor shortage.
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INDEED at THAT time, even the 555 were not available at all. 0 in stock. I needed the LCM: no way. There was only one type in VVIP package …
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This confirmed the shortage issue (bias confirmation?). Right till here?
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I chosen the only one (at THAT time) available (so I even not opened the MMBT datasheet itself).
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Yes it was marquee with S but I opened it’s Datasheet to verify the data.
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Up there is written and reported as you see on my screenshot.
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Having chosen the MMBT in KiCAD, it reported the 1 and 2 inverted compared to the datasheet.
HENCE:
- Knowing that the pin number on a symbol is linked to a foot print pin-by-pin, I chosen for a symbol that had the 1, 2 and 3 respecting the KEC Datasheet.
- Then I assigned it to the only one SOT-23 footprint into KiCAD.
Far to know/imagine/guessing that the pin assignation of KEC is NOT respecting the IPC 7351
(I say it again: if a standard is not respected, it lose the “standard” name, then all combinations should be included)
Of course once delivered, the circuits were not working.
As result: today we’re here.
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Unfortunately the reason they had stock of this part was probably because it is not pin compatible
???????
According to everything that was shown here 2N3904S is pin compatible with MMBT3904.