Ah, I see. I found the problem. This collection should be excluded from the backup. There is a commit in mongodump/mongorestore tools: TOOLS-2537: Ignore config.system.indexBuilds namespace (#242) · mongodb/mongo-tools@d11f1d4 · GitHub. But PBM 1.5 uses an older version of these libs.
In the upcoming PBM v1.6 (should be released in the following days) these dependencies are updated and include mentioned commit.