Thanks for the response. Sorry that the information was insufficient. I tracked the issue down myself.

FYI:
My calculations take in the simulation description in a .csv file, in which the first line is
x-size,y-size,,
of the simulation (the trailing commas are to make space for more columns further down). The first value was being read as a NaN, so it could build the structure mesh fine, but crashed when asked to compute the free surface mesh. This is reproducible, but doesn't happen with all input files.

I still don't know why the first value is NaN. I got around it by adding a 0 before that, so now the first line is
0,x-size,y-size,

Edit:

I opened a working and non-working (without workaround) file in HxD to see if there was anything I couldn't see in Notepad++.
There, of course, is!

The few characters before the 0 are only present in non-working files.