Are different system programs compatible?

This might be a stupid question, I don't really understand a lot of how this works. I just got my printer running yesterday. It's from the Ultimaker brand, which uses the YouMagine website to open-source prints. I tried a couple, they work fine. I tried to print a couple of things from Thingiverse, which is owned by Makerbot, and they didn't work. I just got a big stringy mess. Is there some sort of compatibility issue between different manufacturers (in this case Ultimaker and Makerbot) and if so, can I code around it? Thanks

I'm on a Maker Select Plus if that matters