Hi,
the one R3load running should be the one creating the indexes (this cant be done in parallel).
You could connect to database and have a look at table /MAXDB/INDEXSTATEMENTS, at the end this table should be empty or does not exist anymore.
https://service.sap.com/sap/support/notes/1464560
So just wait ...
an (as root)
sapdb/<SID>/db/bin/x_cons <DBID> sh ac 5
should give you the running threads of maxdb, if there are still some this should be ok.
Best regards
Christian