Nope, you're not doing something wrong. Fact is, pitch tracking has been a sticky point about synth + acoustic instrument setups since one of them played a big part in blowing up ARP in the late 1970s (ie: the Avatar). And the problem is that whenever you attempt to use this, you either have to have a no-foolin' monophonic instrument, or you're going to get glitches of varying sorts. With guitar, you have to cut the flash WAAAAAAY back...hit a second note with the first one sounding, have excess resonance from the other strings, and so on, and you've got glitches galore. The ONLY fix that ever came along that worked are Roland's hex pickup-based synths, since each string gets its own pickup and there also appears to be some circuit-fu that keeps the glitchy issues under control.
HOWEVER...there are reasons to want to use those glitches, and that starts with one Mr. Richard D. James, aka Aphex Twin. He started using the Korg MS-20's "input" section, which contains a pitch tracker, bandpass filter, envelope follower, etc for processing things it literally CANNOT process...like a TR-606. With some twiddling about, the end-result comes out to those squealy, clattery electronic patterns that characterize his early work...and it all comes down to "creative misuse", something I like to call "abuse potential" when it pops up. The MS-20's abuse potential is pretty much off the charts. So if you're getting glitches with the Sonicsmith converter, well...can you use the glitches musically? You might be about to stumble across a whole new sound...