It is not uncommon to have unbalanced VFD input currents when fed from an open-delta (see paper from Yasakawa below).
The line-to-line output impedances of the open delta will not be symmetrical. For one thing, the center-tapped transformer is typically larger and so the impedance across A and B will be lower than that across B and C from the smaller transformer. And the impedance across the "open" part of the delta between C and B will be the highest because the secondaries of both transformers are in series.
Of course, the open circuit voltage on the transformer outputs will also have a major affect on the balance between VFD input currents.
If you don't already have a line reactor and/or DC link choke in the VFD, they could help equalize the input currents.
Line reactors might also reduce voltage spikes and other distortion that could be causing such issues.
Paper frpm Yasakawa:
https://www.yaskawa.com/delegate/ge...PS.01&cmd=documents&documentName=PR.PS.01.pdf
This article is somewhat dated but still has some relevant info:
https://www.ecmweb.com/content/article/20891755/beware-of-linecurrent-unbalance-on-vfds