Have you always had this problem? If it's something you've always experienced with your MacBook Pro 13" and MainStage I'd say it's due to the machine being the 13" model. They're renowned for struggling with MainStage and in particular, for the exact audio issues you've described....especially if the issues are occurring with both your external interface AND the Mac's internal audio. The 13" models are generally underpowered for MainStage's resource demands, although Apple's release notes for MainStage v3.3 say this has been improved. Regardless, I've seen this situation (online and in person) time and again. You'll find plenty of reports on this forum about it.
I suggest trying a completely different (and highly regarded) audio interface and if the same problem occurs, it's almost a certainty that your MacBook is the culprit. I've only used 17" and 15" (after the 17" was discontinued) MacBook Pro machines and have only once experienced something like you've described....and that was due to a low-quality FireWire cable. On the other hand, every single 13" MacBook Pro I've seen trying to run MainStage has suffered from audio crackles and CPU overloads with buffer settings of 128 and less, even from relatively "small" loads eg single Kontakt instruments. You could try a buffer setting of 256 but the latency would be pretty significant. Personally, I can't tolerate latency any greater than 64 samples.