A week ago I forgot to connect 2 out of three vaccum(the big one and the medium one) lines after putting back the stock intake. I felt like my car pulled a lot better, though lacked in the top end a lot more. After connecting them back, I felt like things evened out. Is that normal?

 

That might be due to air entering the intake system behind the MAF sensor. Essentially, you could be leaning out the motor by adding air that the sensor can't "see". At the top of the RPM range, it may have been so lean that it caused a drop in power rather than an increase, but it's hard to say for sure.

Just guessing at this point.

 

does this indicate a problem with the car?

 

I certainly would not drive around with those connections open on the system.

I'd just hook everything up the way the factory did it, and leave it alone.

I'd also say if your car behaves differently with them disconnected....well that seems logical to me. If it's back to normal after you hook them up, no problem. Otherwise you'll have to check into it further.