Toner transfer can be tricky to get working well. Here are the things you need get right for best results:
use toner transfer paper. I particularly like Press’n’Peel Blue. People will say magazine paper works, and it does, but proper transfer paper is better, especially Press’n’Peel
Copper must be absolutely free of oxide, grease and dust. I use an abrasive rubber polisher I got from RS. Dust is an issue as it can stop the artwork making contact with the pcb.
Sufficient temperature ( this is dependent on your printer toner - too cold and it wont stick, too hot and it will smear
My final setup used a temperature controlled hotplate, and a vacuum pump with a silicone sheet to provide pressure. I got to the point where I could have a PCB in my hand in 30 mins. Great when you’re in the middle of a rapid prototyping cycle where you might want to try three or four variants in a day (which I have done). No chinese fab house can do that for you.
I got this process to the point where I could make double sided Kapton flex circuits using 5mil/5mil design rules (thats 0.13mm in metric).
To your specific issues I’d say the missing toner is likely due to not enough heat and uneven heat or pressure. Next most likely is bad copper prep - dust/oxide/grease.