General confusion:
* Confused
* Disoriented
* Bewildered
* Perplexed
* Mystified
* Flustered
* Upset
* Distressed
* In a muddle
Involving objects or information:
* Jumbled
* Tangled
* Scrambled
* Disordered
* Chaotic
* Muddy
* Confused
* Intermingled
Regarding people's emotions or behavior:
* Upset
* Distraught
* Troubled
* Unstable
* Confused
* Uncertain
* Torn
For specific situations:
* Lost (if someone is lost)
* Wrong (if someone has made a mistake)
* Uncertain (if someone is unsure)
* Unclear (if something is unclear)
The best synonym for "mixed up" will depend on the specific meaning you want to convey.