You weren't all the way in gear. Sometimes when the transmission's cold in the morning, it'll stop and feel "somewhat" like it's in gear when it's really not. When you let out the clutch and it go time, the stick'll kick back out.
What I do now is when I get "the feel" that it's not quite there, I keep forward pressure (lightly) on the stick and when you let the clutch out about an inch or two, it'll pop the rest of the way no problem. Finicky or what?
Now, I don't know for sure about your problem with second, but I had one similar. I found I was using too much left angle when I was shifting into second. Again, it's a technique thing. Although natural reaction when you're on the left-hand side of the shift pattern is to hold all the way left, this will cause the shifter to hang on the gate to second. Pull straight back from first and I hit it right every time.