I ran into the same problem when reworking some macros on an old group of mine.

It turned out to be the default keybindings (in Blizzard main menu > key bindings) had ctrl-1, ctrl-2 etc set to something already. I simply unbound them and mod:ctrl worked fine.

If you're using something like Bongos2 for your keybindings it'd be an idea to make sure you've not got them already bound.
Basically Blizzard/hotbar keybindings (e.g binding target self to ctrl+1) seem to take priority over modifiers in macros (e.g. a macro containing mod:ctrl in a button bound to 1) .


One way to test if this is the case is by holding down the modifier key and clicking the macro. If the macro runs properly, you know ctrl+whatever you're trying to bind it to has already been assigned.

I hope that made sense