Why are excess HSA/IRA/401k/etc contributions allowed?

Some institutions enforce the limits, some don’t.

However, one aspect that you may not realize is that they really don’t know what your contribution limits are. Lots of things affect your contribution limits. For the HSA specifically, your limits can be reduced if you are only eligible for part of the year, or if you have another HSA account that you are contributing to. Your limits are increased if you are over 55 in age, if you have family coverage, or if you use the “last month rule.” Sometimes, you won’t know your limit until the end of the year.

Figuring out your limit can be more complicated than it may first seem, and some HSA custodians put that responsibility on the customer, so that they don’t run the risk of doing it wrong or require the customer to give them a bunch of information that they really don’t need to know.

In your case specifically, you should be happy that they allowed the extra contribution, because if I’m reading it correctly, the last contribution that put it over the top was from your employer. Now you can withdraw the excess and keep it. If the custodian had rejected that deposit from the employer, then there would have been a big complication to get it all straightened out with them.