I don't really have much information, but it appears an employer wants to put some money into certain people's health FSAs and not others. I feel like I must be missing something, but all I can think of is that it would only be a problem if the people whose FSAs the employer is contributing to are HCEs, where it would screw up discrimination testing. Is there any issue with doing this on just a "pick-and-choose" basis?

You are correct about the possibility of a problem with non-discrimination testing if the ER FSA credits involve HCEs.

Does the plan include provisions for ER contributions/credits to FSAs? If not, there could be a problem with the plan complying with provisions not contained in written plan document.

Also worth considering is the underlying purpose for the ER FSA credits. Are the funds intended as a distribution of previous plan year FSA forfeitures, or intended to correct funding or claims problems or tied to compensation for these EE participants?

The credits could be intended for a number of purposes and impossible to make a 'compliance' determination without identifying the underlying purpose for the credits.

Aside from a/d problems with HCEs, there should be no problem with a pick and choose basis for contributions. The employer can do the same with insurance premiums, i.e. pay more for some than others.

there may also be COBRA implications. I believe that contributing flat dollar amounts to FSAs results in those accounts being subj to COBRA for the full-term, instead of just for the remaining plan year.

If someone elected COBRA, might the employer have to contribute to their account whether he contributed previously or not?