I have been working on a tree which was mostly input online at Ancestry which had many instances of multiple marriages between individuals, marriage to their own parent, more than one set of biological parents, etc., etc. Here are some useful tips:
1: Give each individual and each marriage a unique ID number in FTM using Tools-->Options-->References.
2: When merging individuals start as high up the tree as possible. Don't merge 2 people who have got parents with different Person IDs. You might want to temporarily rename them sometimes, e.g. John 1 Smith father of James 1 Smith; John 2 Smith father of James 2 Smith. Merge the two Johns then the two James's.
3: Use the Publish menu. The Extended Family Chart with "Include all individuals" will show you (bottom left of the chart) people and families on the tree which have been disconnected from the main body, accidentally or otherwise. The Data Errors Report will list impossible relationships, e.g. born more than 1yr. after death of father.
4: Multiple Parents: It is difficult to identify within FTM all those who have more than one set of biological parents. So, Export your file to Gedcom (.ged) format. This produces a text file which can be opened in Word, Notepad, etc. and can also be imported into an Excel spreadsheet as one column of data. The important thing here is the code "FAMC". The ged file lists all facts about an individual sequentially, so any time that "FAMC" occurs on consecutive rows it means they have 2 sets of parents. Similarly with "FAMS" for spouses. Having identified the individuals you want you can use the Person-->Merge or Person-->Attach/Detach in FTM as appropriate.
Hope this helps a few people.
