Look in your capsule.cfg file.
Remove the ic2:te from this part if you want to capture ic2 blocks with all capsules.
Or only remove ic2:te from here if you only want to capture ic2 blocks with overpowered capsules.
That will atleast allow you to capture ic2 blocks.
But whether it will break stuff, no idea.
I haven't tried the Capsule mod myself, but I came across this:
Which indicates that removing IC2 machines from those lists will cause problems, and fixing it in either mod is apparently impractical until both mods have been updated to MC 1.13 (or later)