Reproduction steps:

(using the default 'test' database)
1. db.dropDatabase() – ensure no data files already present for 'test'
2. db.test.ensureIndex(

)
3. db.test.drop()
4. ls -l mongo data dir and observe that test.0 and test.1 are present (and on subsequent iterations test.2, test.3 etc)
5. restart mongod
6. goto 2.

Each iteration creates an additional test.X datafile even though no data is stored. Curiously without the restart of mongod the drop & ensureIndex behave as expected and no additional data files are created.

I have observed this behaviour with 1.3 release and the 2010-01-13 1.3 nightly.

1.2.1 appears to be ok, only .0 and .1 files are created.