Can you actually break an FPGA by programming it wrong?
It also seems quite possible to accidentally pick the wrong model of FPGA in the synthesis tool, and thus ending up trying to program your chip with a bitstream intended for some totally different model.


Typically the programming software will query the part being programmed for its part number, and refuse to program in a bitstream meant for a different model of FPGA.

The part itself will also generally refuse to start up if programmed with a bitstream that isn't exactly the correct length (and it's very uncommon for bitstreams for different chips to be the same length).


  you could definitely connect the FPGA chip to the rest of the circuit incorrectly. E.g., if you mess up the pin numbers, you might end up with the board trying to drive an I/O pin that the FPGA itself is also trying to drive. 


This is the most likely way to damage an FPGA with wrong programming.

Another way could be to program a very resource intensive design and run it at a high frequency (so that a high power is consumed), and then run it on an FPGA without an adequate heat sink.


  Do the I/O pins typically have any "protection" against such a mistake? Or will the chip just fry?


Output pins will "often" survive a short circuit condition for a few seconds or even minutes. But nothing is guaranteed.