It's hard to answer such a broad question. It would be better (in general for any question posted in QlikCommunity) if you had a specific example where a QlikView / Set analysis limitation could be analysed.
Regarding your question, one limitation I can think of is that set analysis is evaluated once per chart/object and not per row, so if you need to do that, you'll need to find a better way of implementing that kind of solution. However, with advanced searches inside set analysis you can filter all the records that fulfill certain condition. So, this is the nearest you can have in order to get to work set analysis per row,