Your mileage may vary - but - when I deleted a whole group of people in a copy of a tree - the delete process deleted all the people - and left all the marriages/families behind ;-)
It is easy to see such rubbish in the resultant tree (I am using FTM 2014). Export the tree as a GEDCOM and look at the FAM records. A FAM is a family and may or may not contain MARR (marriage) records. If you see a FAM with no IND (individuals) then something has gone seriously wrong. You can look at a GEDCOM extract with good old NOTEPAD etc.
In the test I did, I had 250 odd FAM before I started - and 50 odd real FAM when I finished - and 200 odd FAM with no IND in at all. Compact the database achieved nothing - the next GEDCOM export proved that the phantom FAM were still present in the database.
I guess this means that the program has been written by programmers who do not understand referential integrity ;-)