This was mostly through-hole board, which were fine, but have several 0805 SMT resistors on the back and pads were not exposed, see the image. I ordered 400 of these boards 
Good news is, the SMT parts are optional and will be used rarely.
I tend to think your gerber file set was missing the solder mask file or the solder mask file did not have proper mask generated.
Always do a sanity check on the gerber files!
If the gerber files are faulty, check the SMD footprints. They may not contain the check-mark for the solder mask.
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This is the default 0805 SMT footprint.
I see, the checkmarks for all technical layers on all SMT pads in Edit Pad feature are turned off. Thank you, madworm, for pointing this out.
This is beyond stupid ! It has great potential but silly things like this make Kicad a hobby grade software. Perhaps I put too much faith in CERN brand.
Default from which library? I checked default GitHub library and those are OK. Donāt know about the libraries installed on the computer, I personally donāt use those and donāt even install them.
As MADWORM saidā¦ always study your gerbers using the gerber viewer. You canāt just trust components made by someone else. I donāt think you can blame KiCad the program. Itās a fault of the individual foot print you used.
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This problem has nothing to do with CERN and is probably not even a problem due to KiCad. If someone creates a defective footprint definition KiCad has no way of knowing this.
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Itās a library that came with latest Kicad stable install for Windows. There was no downloaded component used. dwight_m, I donāt care who in the developer chain is at fault, quality of included libraries is factor in overall software package quality, this one has potential but does not stand up to likes of Orcad or Eagle.
Why not compare it to Altium while you are at it? Then you can really show how it doesnāt compare. If you consider the ratio of functionality per dollar then KiCad wins every time 
I agree with you about the footprints though. Those had to be verified before creating an installation package. But they werenāt. If you stick around you will see that you can work with KiCad you just need adopt a new ideology. You need to be slightly paranoid and always double check anything the program does.
Zero cost is misconception, time, botched boards and extra revisions are not free. In all fairness, I was not looking for free, but there is nothing in-between $1,640 Eagle Pro and free Kicad right now (Eagle Standard is not suitable, I need larger boards). I understand packages like Altium or Pads start at $5-10k for barebone and can go through $20k/seat or higher and productivity and bugs/feature ratio may not be that much higher than Eagle, diptrace or Kicad. I am not planning to do complex designs, max LQFP64 and staying in 2-layer domain for now.
I like several aspects of Kicad, for example detachment of footprints and symbols, etc. Iāll stick around, and inspect gerbers before sending them out.
Spinning 400 boards without prototype or at least visual verification of fab outputs beforehand seems very strange to me.
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I didnāt say free, I said the ratio functionality/dollar is still better than anything out there. I would agree that ordering large quantities of boards without getting a prototype done first is not the way to do it regardless of which package you use. Just as easily couldāve been a mistake that you made.
Other than that, I would agree - if you want it free, better prepare to pay for it.
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So, this same thing happened to me. The solder mask layer(s) are still confusing to me on how they work and whatnot.
I figured out what I had done wrong. I had disabled the solder mask layers when I first started working on accident. I went back later and enabled the solder masks layers, but for some reason, the solder mask wasnāt āgeneratedā for the parts I had changed while the solder mask layer was disabled.
The strange thing is that the solder mask layers are always blank when I am working on my project, but when I make the gerber files and view them with gerbv, the solder mask layer is populated and looks perfect.
Does anyone know what is going on here? Sorry if that explanation was a bit sloppy as itās a complicated situation to explain. I can make some screen caps and post some images if needed.
The āsolder maskā is a negative layer, so you only have marks where you want the copper exposed. In KiCad if you disable the mask then nothing will be exposed, but if the mask is enabled then the marks are generated when you create the Gerber files.
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Do you work in Legacy or OpenGL canvas (or both)?
Legacy doesnāt show the Soldermask and OpenGL shows an inverted version to what it will be in reality:
The layer viewer settings only affect visibility in the canvas and for printing.
The CAD models and gerber plotting should not be affected (and IMHO never were affected) by thoseā¦
What does ''the parts I had changed" mean, i.e. what did you do?
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I added a few resistors to the board. When I went back and re-enabled the layers, it didnāt recognize that I had added resistors while the layers were disabled. Every pad on my board was exposed properly, except for the resistors I had added during that time.
Iām not saying that I know how it works, just that that is what happened to me. Iām still experimenting with it trying to figure out what happened and what causes something like that.
Also, yeah, I have been using the Legacy viewer. I had no idea that the OpenGL canvas showed that. Thank you!
Wow. I was wondering why I couldnāt draw on the solder mask layers at all. Then I switch over to OpenGL and BAM! Suddenly, I can draw all sorts of stuff on the mask layer.
You just saved me a ton of headaches. Thank you for the suggestion!