Initially reported on the mailing list: https://lists.launchpad.net/maria-discuss/msg02495.html .
Reproducible as described.
Dataset: salaries table in the employees sample database.
Statements that exhibit the incorrect behaviour:
I also saw the mentioned 350% and some other values, e.g.
MyISAM looks reasonable (2 stages, below 100% progress).
Not reproducible on 5.5.
10.0 has a different problem – progress for InnoDB tables is not reported at all.