In full game runs, if a mission starts you with the weapons you ended the previous mission with, your time for that level cannot be submitted as an IL time.
List of Halo levels with weapons carried over:

HALO: CE
None

HALO 2
Metropolis
Oracle
Regret
Quarantine Zone
Great Journey

HALO 3
Tsavo Highway (unless you end Crow's Nest with the Hammer)
The Storm
Cortana
Halo

HALO 3: ODST
Data Hive
Coastal Highway

HALO: REACH - Scoring is off so no times can be submitted.

HALO 4
None