120928-1139 EDT
I do not understand your description.
You have a transformer with a neutral that is not grounded. Thus, this implies that none of the wires from the transformer secondary (ies) have an explicit connection to earth. When you use a "tester pen" it is capacitively coupled to your body and your body is possibly capacitively coupled to earth.
Note: there are both resistive and capacitive leakage currents from all of the secondary wiring to earth, and thus, possible paths for current to your tester.
But if I had you stand on a a conductive plate that was connected to 120 V relative to earth, then your body would be near the 120 V level relative to earth rather than at ground potential. So I can not be too sure that your body when using the "tester pen" is really referenced to earth, but it probably is.
Assume your body was referenced to earth and all transformer output wires are floating from earth, then there is at least the possibility of capacitive coupling from the transformer primary to the secondary that would supply enough current to light your tester. There are other possible explanations as well.
I do not know what this meant "the ground had a little bit of voltage on it". Was ground the EGC or the neutral? If it was the neutral, then my above explanation is a possible reason. If it was the EGC, then there was an EGC wiring problem or your body was not referenced to earth. A few other possibilities, but not likely.
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