How ? it is invisible?
Nah joke aside, how do you be stealthy while under the effect of a fly spell?
Not flap around with your arms so fast?
And what exactly is the PC perceiving as a target? a flimmering like in predator?
Dispel magic needs a target and that implies to me visible somehow.
At least that is a hefty perception check to be involved for this. But as I said before I am not the judge on your tables, but I really would like an answer to my two questions in case I would like to rule it like that on my table, how would I explain these two issues to my PCs?
And no, I will not take sage advice for an answer in case there is some because it surely was not meant for this special case. The general philosophy of your rule makes the invisibility spell pretty useless except for characters who rarely need it because they are stealthy already.