I've installed a bunch of mods, created a merged patch, and then I'm getting a CTD before the game main menu. So I looked at my mods with FOMM and I see many of them have this warning message in red:
"WARNING: This plugin has the file extension .esp, but its file header marks it as an esm! "
Is that the problem that's causing me to crash? How can I fix that?
Thanks in advance!

That's just a result of the MasterUpdate function. Perfectly normal.

Post a list of your mods from FOMM. Maybe you're missing an important master file.

Fallout3.esmCRAFT.esmCALIBR.esmProject Beauty.esmFO3 Wanderers Edition - Main File.esmMart's Mutant Mod.esmEnhanced Weather - Rain and Snow.esmXepha's Dynamic Weather.esmCompanion Core.esmRobCo Certified v2.esmStreetLights.esmCRAFT - Activation Perk.espFO3 Wanderers Edition - Main File.espFO3 Wanderers Edition - Followers Enhanced.espFO3 Wanderers Edition - Optional VATS Halftime.espFO3 Wanderers Edition - Optional Restore Tracers (automatics only).espFO3 Wanderers Edition - Optional Free Play After MQ.espFO3 Wanderers Edition - Alternate Travel.espFO3 Wanderers Edition - Project Beauty.espFO3 Wanderers Edition - Project Beauty (Followers Enhanced).espWeaponModKits.espWeaponModKits - FWE Master Release.espEVE.espEVE - FWE Master Release.espEVE - FWE Master Release (Follower Enhanced).espEVE - FWE with WeaponModKits.espMart's Mutant Mod.espMart's Mutant Mod - FWE Master Release.espMart's Mutant Mod - Project Beauty + FWE.espMart's Mutant Mod - Project Beauty.espMart's Mutant Mod - Increased Spawns.espMart's Mutant Mod - Hunting & Looting.espMart's Mutant Mod - Feral Ghoul Rampage.espMart's Mutant Mod - Natural Selection.espMart's Mutant Mod - Zones Respawn.espMart's Mutant Mod - Tougher Traders.espXepha's Dynamic Weather - Main.espXepha's Dynamic Weather - Rain.espXepha's Dynamic Weather - Sandstorm.espRealistic Interior Lighting.espStreetLights - Wasteland.espRobCo Certified v2 Version Updater.espEnhanced Weather - Rain and Snow in Fallout.espEnhanced Weather - Weather Sounds in Interiors.espEnhanced Weather - Radioactive Rain and Snow Plugin.espEnhanced Weather - Sneak Bonus during Storms.espDarNifiedUIF3.espmymergedpatch.espTotal active plugins: 48Total plugins: 48

I'm just trying to play FWE with all the recommended mods.