TSA has no authority to confiscate them. TSA also had no basis upon which to ask you to surrender them. Suggesting that a screener wanted them for personal use or resale is pure speculation, but nonetheless within the realm of possibility.

While TSA is not supposed to be on a fishing expedition for items besides weapons, explosives, and incendiary devices, if they found a quantity of medication which appeared to easily outnumber the quantity prescribed on the Rx label, then it would have been possible for them to summon a police officer. You may not have wanted to be in a position of trying to explain to a police officer that pills you were carrying in excess of the quantity on the Rx label were, indeed, legitimately prescribed... after all, from the evidence in front of them, you're carring narcotics for which you don't have a prescription, and they may be quite reluctant to take your word otherwise. So in this case, even if you were telling the truth, escalation may have not worked well in your favor.

To avoid a similar issue in the future, always carry a prescription bottle that has the prescribed quantity printed on the Rx label, and don't carry more than that. This alone should be sufficient to deter any challenges from either TSA or law enforcement.