Once the design engineers changed the strategy, to include EMC as part of the initial design, the problems either went away, or were of a much easier nature to solve.
that does not happen when you try to "make it cheap"

All lines entering or leaving the kit should have suitable EMI filtering, and the enclosure should also offer EMI sheilding, and pay special attention to the power supply arrangement as this is often a good way for EMI to become coupled onto your kit. Also consider transient supression on the signal and power lines.

Also proper PCB design with properly designed power and signal planes, and supply decoupling will also reduce the suceptability to EMI. This can lead to the need for 6 or more layers, most 4 layer boards are actually poor for EMI.

restated in one sentence:

If you 'save money' you WILL have EMI problems if your unit is exposed to EMI.

Yes, the amount of effort (money) put into EMI protection is, of course, depending on where the unit is to be used. But anything that goes on the shop floor, or similar places, will need all measures taken (however 'cheap' you want to make it) or you WILL have problems.

It is clear from this thread
-I don't enclose the board or CPU in a metal enclosure in order to protect it from EMI traveling in the air.
-I don't have GND fillouts on top solder. </1> = one or two layer board
-My board doesn't have a ferrite at power inputs.
that the OP tried to save money and lost.

Erik