it appears your accountant screwed up. he should have gone by what is on the W-2, not the 5498. the W-2 should show employee and employer contributions. as long as the total on the W-2 doesn't exceed the max for that year there is no excess to be withdrawn.
I should also point out that if the employer will not deal with employee contributions, nothing prevents the employee from making his own contributions to the HSA. they are reported on line 2 of form 8889. employer contributions appear on line 9. as long as the combined total does not exceed the max, there are no penalty taxes.
