Naruto
Bee
Guy
And Kakashi were all fighting Obito at the same time and couldn't scratch the guy, now all of a sudden Kakashi fights him alone and actually has a chance lol what?
Obito's ability has two facets:
1) His Kamui ability makes him nearly immune to all attacks (ninjutsu and taijutsu) UNLESS one of the attackers also has Kamui and knows the secret to the technique (unlikely)
2) His unique physiology means he can use his MS techniques as much as he wants without losing chakra and without going blind (unlike Kakashi, who wastes a LARGE amount of chakra to use Kamui).
It's no surprise in his fight against Naruto, Bee, Guy and Kakashi that he was unharmed for most of the battle. His ability makes himself immune from most of their techniques (there are no genjutsu users in that bunch) and it wasn't until late in the battle when Kakashi figured out his technique (and he figured it out on accident). After they figured out the secret, they WERE ABLE TO HIT HIM and did it several times (Naruto rasengan to the face, Kakashi punch to the stomach, etc).
However, things are a little different now. Inside the pocket dimension, Obito CANNOT USE KAMUI in the same way. Here's how Kamui works: When attacked, Obito's Kamui sends part of his body to the other dimension temporarily. However this current battle is happening entirely inside the pocket dimension, and there is nowhere safe for Obito to send parts of his body to avoid Kakashi's attacks. This means that for this battle, Obito's most powerful attack is rendered useless, and he IS ON MORE EVEN FOOTING WITH KAKASHI.
This situation is complicated, but if you pay attention, it all makes sense.