So i open up my Pipboy after i had just leveled up my guns to 60 and look at it and it says - 59 (-)... where did the negative come from and why did it take away a point? this happened for a bunch of them. two of the ones had +'s after them. also on the S.P.E.C.I.A.L my endurance was at 5 and i looked at it and said 4(-)

why is this?

There's an EFF tab on the first status screen, you can use that to find out.

As Nessh said. It could be from any number of various effects; suffering from drug withdrawals, a crippled limb, negative effects from certain consumables, radiation, etc.