Yes and that is the key. To learn to distinguish between normal fatigue\discomfort and the start of an injury that will end up in a disaster if you do not know when to STOP!
I too got Top Of Foot Pain once by running 2-3 miles for two days on sidewalk concrete. apparently it is too compact for my feet. Within a day I knew this was not just a bit of fatigue and it progressed to a painful condition for a few days and a 2 week recovery.
Luckily I stopped when I did. If I had pushed on, it would have turned into a stress fracture or worse. As it is I recovered within 2 weeks and ran my full 1/2 and a full marathon less than 3 months later!
Like I tell people that I'm teaching, I value and enjoy my rest days even more than my run days. For these are the days where you recover, and enjoy the feeling as my feet go from tender\sore to strong and healthy.
Yeah, TMTS definitely isn't much fun. Definitely ease off on the minimalist running. I got top of the foot pain from doing too much too soon. Thankfully it was just strained muscles vs a metatarsal stress fracture. I was sidelined for two weeks. After that I did a seven month transition to minimalist shoes (VFF and RunAmocs) and now I'm running full time in them and have even completedd three half marathons. A slow transition is definitely worth it.