You need to provide much more info to get a quick answer.
Post a screen grab of your render settings and output module from the Render Queue, or from Adobe Media Encoder if you're outputting there.
What video codec are you rendering to? What file format? How big is your rendered file size? What software is telling you that it is 13 minutes long? What software are you using to play it back?
Im playing it with VLC media player and thats what it says its 13 minutes,
I am outputting it to AVI format with no compression as I do the compression with Handbrake afterwards.
The file size is 4.74gb and can sometimes can go up to 15gb.
Sorry I cant send a screen grab
Most hard drives can't play back uncompressed video files because they are too big, especially if they are high definition.
If you encode one of the problem files with Handbrake, does the resulting file also have the same problems?
You have not provided any exact render settings or system info, so nobody can gauge your results. As Andrew said already, uncompressed content can be taxing on the system. The duration not being reported correctly on the other hand could have all sorts of causes like you messing up the framerates or CoDec issues with your source files, audio problems or hardware acceleration issues, none of which we can know since you have not provided any info.
Is your comp in After Effects 1 minute long? Maybe your comp is 13 minutes long?