The sms threads in the Messages app aren't always in order. I imported my messages from my N900 and those are out of order. However this occurs in other instances as well, sometimes I'll receive a text and my reply will show up before it in the visual order of the text bubbles thus conflicting with the time stamps. Does the Messages app not order the text bubbles by the timestamps? This can make reading a conversation with someone hard to comprehend and confusing. Would it be possible to make a app that could scan through all the threads in Messages and re order the messages in relation to their time stamps?

Sounds similar to the issues being discussed here....
https://harmattan-bugs.nokia.com/show_bug.cgi?id=113
See all the comments not just the title, add your vote and input.
If you feel your issue is totally different, search bug-tracker to make sure it's not lodged.
If you can't find anything like your issue, then lodge a new ticket.
If you feel it's not so much a bug as a design/feature limitation...
Be sure to lodge it as a "enhancement request", makes the devs jobs easier.