Hi,
Okay, there are a few options to get past this:
1) You very likely would be okay with setting pmin = 5000, instead of 1000. This would still use the levels up to 50 hPa, and unless you need to use the data above that (which most people don't), you should still get reasonable results with this setting. I tested this and it works (while I also tested setting to 1000, and I see the same problem you did).
2) There is a utility in the WPS/util/ directory called "mod_levs.exe" that will allow you to specify the levels to use for a dataset. Since the GFS data beginning at 2019-06-12_12:00:00 has more levels, you would need to do this for the data starting at that time. You can read more about that option here: https://www2.mmm.ucar.edu/wrf/users/docs/user_guide_v4/v4.1/users_guide_chap3.html#_WPS_Utility_Programs
3) Instead of using analysis data, you could use the forecast data, where if the data are initialized at 00 UTC on the 12th of June, and are forecast out 24 hours (or whatever) from there, then all the times should have the same levels. The problem with this is that you don't have the final analysis in the data, so the accuracy could potentially be worse.