If it were a gui Control, I would say most likely culprit is mousefilter property...
There might be another control above it that's stealing the mouse move event... you could check the z-index of the area2D.
Also, the collision shape node might be disabled.
Not sure if relevant, but the input/pickable property might be a factor
Also, what event/signal are you using for this? you should probably be using the Area2D's mouseentered event for this, or the _input() event if you want more control
Seeing some code would be really helpful. I would debug to see if maybe the event gets called, but the code is not executing the way you imagine.
Also, there's a debug-draw collision shapes setting somewhere that could help... maybe the area is not where you think it is.