The shifter can be pressed down in gears 3 and 4 when in manual mode, and from neutral to reverse. The reason it can push down in 3rd and 4th is so that it registers as different buttons than 3rd and 4th gear in sequential shift mode (dual-layered buttons, if you will). When you switch to sequential shift mode on the shifter, you push the stick in and turn the knob, locking it into the pushed-in position and only shifting back and forth. When doing that, it registers as 1st and 2nd gear for some odd reason.
No problem whatsoever. It's just a (annoying) feature.