Health Savings Account Employer Limits

We have setup a HSA that has 2 employer contribution limits, one for EE only that is $500 and one that is for all other coverages that is $1000. We preloaded the employer contributions on the first check of the year for anyone that enrolled in the High Deductible Medical plan during open enrollment. Any new hires that elect the Hight Deduct Med Plan has their employer contribution deducted each pay period. We are having issues with the employer contribution limits from stopping for all the employees we preloaded on the first check because we can only