sqrt(x) returns the positive square root of a real number x. For example, sqrt(4) returns 2, but -2 is also a square root of 4.
sec(x) returns the secant of the angle x, which will be positive or negative depending on which quadrant x is in.
So to answer your questions: 1. the discrepancy is due to the sqrt function picking the positive square root. 2. they are both correct.
The identity in question is more correctly written as sec(x)^2 == 1 + tan(x)^2 (the square of both sides of the one you stated), which does not have the ambiguity due to the sqrt.