What it sounds like you did was to take ownership of the stock and sell it in your own name. Because you receive a stepped up basis equal to the share price on the day she died, you probably have only a small capital gain or even a small deductible loss. When you report the sale on your tax return, you will also report the withholding, and it will come back to you as part of your tax refund, or it will offset other tax you owe.
Your question does not make a lot of sense for two reasons.
1. Sometimes, the estate owns the shares and could have sold them directly. Estates are legal entities that can do any kind of business that a person can do. However, if you were a designated beneficiary on the account, then the shares went directly from your mother to you and were never owned by the estate.
2. If the estate did sell the shares, the estate would owe more capital gains tax than if you inherit the shares and sell them in your own name, so there is rarely a good reason to do it that way.
So the broker may have protected you from your own mistake regarding the capital gains tax. However, if you believe it was important that the estate sell the shares instead of transferring them to you first, or if you don't understand why the shares had to go directly to you and you are still concerned about it, then you may be in over your head and need professional assistance managing the estate.
