These do look like bugs which I recommend reporting.
Two workarounds for you to try:
1. Keep raster names <= 13 characters. A commonality I'm seeing here are long raster names. This has to do with historical limitations in some tools.
2. I have always gotten better raster processing performance (and avoided weirdness) by using file based rasters, that is, esri grid, or these days, .tif, stored in a folder. I think gdb rasters are great for read but not as good for writing.