I also ran into this bug. In my case I have ⇪ as hyper key set to right ⇧⌃⌥⌘. It works in all other applications, but not for sending shortcuts to Teams. If I skip the hyper key and just use ⌘X to send ⌘Y it works, but using the hyper key doesn't. It doesn't matter if I just send the plain key, or if I send it specifically to Teams. Other actions work: I can use hyper key triggers for menu bar or context menu items, just not with shortcut key actions. It seems Teams somehow sense that there are other modifiers active, and thus mis-interpret whatever key I'm trying to send.
My solution was to add a small delay at the beginning (long enough for me to be able to release my fingers from the keyboard before the shortcut is fired), and then send the shortcut specifically to Teams.