Repairs with vnodes is likely to cause a lot of small SSTables if you have inconsistencies (at least 1 per vnode). Did you have any issues when adding nodes, or did you add multiple nodes at a time? Anything that could have lead to a bit of inconsistency could have been the cause.
I'd probably avoid running the repairs across all the nodes simultaneously and instead spread them out over a week. That likely made it worse. Also worth noting that in versions 3.0+ you won't be able to run nodetool repair in such a way because anti-compaction will be triggered which will fail if multiple anti-compactions are attempted simultaneously (if you run multiple repairs simultaneously). Have a look at orchestrating your repairs with TLP's fork of cassandra-reaper <http://cassandra-reaper.io/>.
