This is a rather new warning in the code.

When you invoke the input generator one thing that is done is the detection of symmetries in the unit cell. Symmetries may spped-up and stabilize calculations. But most of the time, you also don't rely on them. You have two optione:

1. You adapt your input such that all values in it are provided with higher precision, which may result in more symmetries detected.
2. You ignore the warning and go on with your calculation. To do this you can either invoke inpgen with the additional command line option "-warn_only" or, as explained in the terminal output, put a file "JUDFT_WARN_ONLY" in the directory of the calculation. If you proceed in this way the warning is still written out, but the program proceeds and writes out the Fleur input.

Good point. I just made a commit to make this hint more explicit:

https://iffgit.fz-juelich.de/fleur/fleur...3f73f78c915cdcd

It will be available in the next Fleur release.