It's difficult to offer any concrete solutions to your problem without
knowing exactly what is happening at each stage, but there are two possible
areas of difficulty here.

Firstly, how are you numbering the document in the original? For reliable
numbering, you need to use numbered paragraph styles - or if that's not
possible then maybe ListNum fields or a List Style. Don't use either the
numbering toolbar button or Format > Bullets & Numbering.

Secondly, you need to make sure that everyone understands what to expect
with track changes. The numbers will *not* take their final correct value
while the changes are 'marked up'. If users try to 'correct' the numbering
at that stage that could be a reason why things fly apart when the changes
are eventually accepted/rejected.

See http://www.shaunakelly.com/word/numbering/OutlineNumbering.html for
instructions on setting up numbered paragraph styles.