Upgrading MongoDB ReplicaSet to 3.0 causes BSONElement: bad type 108
Found the answer:

In 3.2 WiredTiger is the default storage engine. So I had to remove existing databases (/var/lib/mongod). After starting mongod it will replicate from the primary member.

I accidently updeted directly to 3.2.9 and it worked. That was the reason that WiredTiger was default engine.