A complex issue. A flushing is most often a procedure to leech out excesses, and you run a lot of water through... Overwatering is like djruiner says to constantly keep it too wet, which more often than not induces rot.
If the plant is sickly when flushed - which it often is - the flush might just kill it or induce rot, cause it's not capable of drying up the media by drinking afterwards. Then the flush made it overwatered...
Small plants in big pots, same problem.
Do you use perlite? 30% is nice, and increases the aeration so that the risk of rot decreases substantially.
I never flush I water with 10-20% run-off instead, to rid the media of excess unused nutrients and metabolic waste-products that otherwise builds up. But this way of doing it is dependent of correctly matched plant and pot-sizes, and perlite enhancement.
I would of course advice you to go my route with perlite, correctly sized pots, and run-off when you water, but opinions is like assholes...