Hmmm, firstly I'd make sure you have the current version (it should say the version number on the title screen.) There was a progression issue with Shallot's cutscene flags in investigation 3. I patched it out back in December, but I figured I'd mention it just in case.
Otherwise, to complete all of Shallot's stuff in that section, you have to
- Complete all of his initial talk options
- Complete all of Mateo's talk options (in the conference room. The Costume Chest evidence will be updated during this)
- Present the updated Costume Chest to Shallot
- Use his new "what you witnessed" Talk option
- Search the Butchery and choose the Fire Escape
(Also, if you were on the older verision, you may have to do the last three steps again. Sorry!)
Hope that helps ^^