As demonstrated in https://en.wikipedia.org/w/index.php?title=Wikipedia:Sandbox&oldid=645888452 #iferror correctly suppresses the scribunto error, but still adds the error category. I feel this behaviour is a little odd, it's like throwing an error and catching a bit of it. Whilst there are arguably better ways to handle scribunto errors, as the conversion from wikitext template to modules is always going to be a gradual transition users should be able to address this type of issue as they get to them not be forced to have a category full of false positives.
This might cause a similar issue when T25959 is fixed as the parser function error categories are added through interface messages instead of with addTrackingCategory like Scribunto.