Not SquareEnix support here, but reaaaally quickly here: the MacOS version of FFXIV is built atop CodeWeavers Crossover, which is itself built atop WINE. There are two potential issues with how WINE (and thus Crossover) handles mouse.

1) If the WINE layer is running as a window but the Windows application within WINE is running full-screen, it can cause mouse events to get lost.

2) If you have two monitors, if you move the mouse cursor to the monitor a WINE application is not on while the application is in the background, it can cause the application to no longer be able to read mouse events.

If either of those applies here, that might be your underlying issue.

(There's another thread with some discussion about it over here.)