fluffy82 comment

"the gedcom seems to have almost 12 000 people in it... Who are those 2 000 extra people? :)"

I don't know the complete answer to your question but it could be due to the following: An example.

When you merge two people in FTM, it ends up choosing one of the two "ID Numbers". It never uses [reassigns*] the other ["discarded"] ID Number again. That is why if you check your maximum ID Number in FTM you will find it is larger than the number of people in your data base

I have had your situation when I, for example, export my data base via GEDCOM to say Legacy

Legacy shows that I have more people in my FTM 2014 data base than FTM shows --- It shows the number of people I actually have plus the ID numbers not reassigned by FTM [in other words it shows the total ID numbers.] And when I check it out some of those so-called extra people they don't have names assigned to them

My comment above is not very well explained and perhaps other people who have noticed your situation could do a better job of explaining it

* I can't remember if there is an option in FTM to never use [reassign] the ID number that is "discarded"