This seems to be LWJGL related.

First: Some uses of "control" now seem to be mapped to "apple/command". This sort-of makes sense. Microsoft windows uses ctrl-C for copy, ctrl-v for paste; Apple uses command-C for copy, command-V for paste, etc. So, the LWJGL seems to be mapping ctrl to command in many/most cases.

Ctrl-"drop" drops a stack on windows.
Command-"drop" drops it on the mac.

(... is there any other use of control in vanilla?)

In fact, I just found another issue here. After command-"drop" (I have "drop" bound to a key; this might be different on a mouse), the "drop" key does not work once. I have to press it once to "clear" it, before it is seen to work again.

When starting up, I normally find the "command" key stuck – the first time I try to use it, it does not work. Additionally, any time I use command-tab to switch to another app, and then back, it is stuck again.

(This is not all cases. I can map a keystroke command to "control", and it still works. Optifine, for example, maps zoom to control by default (I remapped it to Z before testing.))