Personally, I don't know of a 'liquid linoleum' on the market. If your floor is new, I'm gonna assume that when you refer to linoleum you're refering to vinyl.
Going with this assumption, talk to your installer or the mfgr. as to what to do (if you don't get any real help on the Forum.) If they don't have an answer, if you're not talking about a 'chunk' that's been damaged, I'd try Seam Sealer. Make sure when you talk to the retailer, installer, and/or the mfgr. you ask, "By the way, what's the proper Seam Sealer for my floor?" This way you're one step ahead if it's a last resort. If you go with filling with seam sealer, make sure the gouge is clean.
OH, before I forget, hopefully you have some remanents from the installation. (Usually there are some left over by the installer to keep around in case you end up having to replace a small section, which by the way, you can do in this case.) Take a scrap piece and gouge it just like the one on the main floor. Put some seam sealer in the gouge and let it dry for a couple of days. If it's not tacky, go for it! In the meantime, I'd put some Painter's Masking Tape over the gouge to keep it clean. Don't use regular masking tape. It may leave some residue around. It would just make sense that someone out there makes a liquid vinyl repair product for just what you're describing. Ask around.