The "decommission" function has disappeared from the "command" list for some ships. I just saw it for two ships I got from anomalies, a "defender" and a "gunboat". The list looks like it has room for the function at the top of the list, but it is not displayed. Since it appears at the bottom of the list for ships I designed, perhaps it is not displayed because the list is being shifted downward by a blank entry for the first item.
The function still appears in the "details" panel for the selected ship.
And now, a couple of turns later (without a restart) I got a core ship (a Battle Axe this time) from an anomaly and the ship's command list displayed correctly.