The same problem happened to my online map. Everything was running fine (albeit a bit slow), then after the 25th layer added (all less then 1k records) - the file wouldn't open. Sometimes message said "corrupt file". I finally could open the file with Chrome.
However, I essentially had to start over, parse my entire map project into several, given this limitation (I too did not see any limits to no. of layers, posted anywhere). This caused me alot of grief, and a lot of extra time (20 hours to be exact).
Can ESRI post better guidance to this effect?
Thanks. I do appreciate the product!