Most likely the seal that gets out of place or cut/torn/worn when reinstalling the top by not being careful.
In reality that seal should be treated as a maintenance item even on a top that does not get removed regularly - the rubber on the roof area sees some intense heat and thats gotta put a beating on the life span of that seal.
Once it cracks and deteriorates it can hold water and therein lies the problem.
Just like door weather stripping needs replacing from time to time to keep a good seal so does the rubber for the tops.
Just my guess/opinion - I could very well be wrong…