I have some troubles seeing all online aircraft on VATSIM in Navigraph Charts. I do see most aircraft, but not all. I first thought it occured mostly at EHAM which is below sealevel, but this morning I even didn’t saw some A340’s at EDDF.
I see that you posted in the Charts > Desktop category. If you are using the Desktop app, this is a known issue that will be fixed in the next release (soon)!