Employer maintains SIMPLE IRA at a financial institution. All the accounts under the SIMPLE is at the same financial institution.
Employer sent in checks to financial institution along with breakdown/allocation sheet.
Employer made a mistake (clerical error) and gave instructions to deposit more than the correct amount to one participant’s account, and less than the correct amount to the other participant. (One person got too much, and the other got too little).
These were employer matching contributions
Can the employer just send a letter to the financial institution to make the adjustment?
Is this affected by the irrevocability of IRA assets?

If the error is timely reported by the employer (details help), the financial institition will generally make "correcting" entries. Otherwise, make the necessary contribution and report amount on participant's W-2 (as wages) for the year. It would help to inform the employee that a prohibited excess contribution was "deemed" made to his SIMPLE IRA and should be corrected. Perhaps the employee will return the funds or the the employer will likely offset the amount from future wages.

If the error occured this year, and both participants are still making contributions, I would just make an offsetting correction with the next deposit. If it was from last year...well, on the couple SIMPLEs that I have the misfortune to be involved with, I get the data pretty quickly after the end of the year so we'd know pretty quickly and would fix it the same way. If for some reason that doesn't appeal to you, you need to contact the financial institution and ask them how to fix it. They'll probably accept a letter of instruction.