The IDE allows users to change the board while compiling.

If the user clicked Upload, after the code is fully compiled for the old board, upload is started using the new board setting and an incompatible HEX file compiled for the old board. For example, code compiled for Arduino Uno can be uploaded to Arduino Due (if a Due is actually connected at the selected serial port).

This problem much easier to reproduce on slower Windows computers, where the compile process takes enough time for the user to change settings while the builder is still running.