It might be that your stored procedures aren't cleaning up the temp tables they use properly.

It's a good idea to use

IF object_id('tempdb..#yourTempTableName') IS NOT NULL DROP TABLE #yourTempTableName

at the beginning and end of any procedures/DTS/jobs that use temp tables.

Check this article (or search Google) for more info: http://stackoverflow.com/questions/6623846/why-are-temporary-tables-not-removed-from-tempdb-in-sql-server