My guess is that it is telling you the truth. If everything is working correctly this might indicate that your antenna is a tiny bit too long… or it is in an environment that is affecting its resonate characteristics. *Depending on the antenna and where it is mounted*, coax length can sometimes be a factor in resonance while sweeping the characteristics.
The TG can be set to operate on a single frequency and the accuracy could be checked with a frequency counter…
I have found my SA/TG setup to be very accurate and have used the combo to check and tune critical frequency dependent cavities.