OP isn't giving any information for instance frequency.
Keeping PCB tracks short is a good idea but some cm are OK.
Issues are too specific to each circuit to give good generic advice. For instance cooling grid will emit EMI to a degree that a temp. sensor (NTC) connected to small LCD thermometer will actually shut down the same!
Solution: inline 1x 330 uH- issue solved.
You should have an ability to think into the circuit, and should build a prototype, before you layout a PCB.
Cracking point #1 is the storage coil (or the flyback transformer).
If it is not the right one, efficiency won't be good.
The OP should give information if a schematic to use already exist (or not).
Or all advice is only guesswork.