I think I have figured out my problem, and I thought I would post this on here in case anyone else is experiencing this. I have had problems while using the Kreg Jig, with screws popping through or splitting the wood with 1x material. For example, I was joining 1x3s side-to-side to create a larger, flat piece of wood and the screws popped up through the flat part of the wood. But I didn't have any problems when I was making 90 degree joins.
I think the problem is when I am screwing into the wood sideways (drill is almost parallel with the floor) rather than from above the pocket hole (drill is almost perpendicular with the floor). There is only 3/4 in of wood, so if you don't get the Kreg screw in there just right, it will pop through. It is much easier to do this when the drill is aimed at the floor.
This is only my second project and I had this problem with my first also. I could have prevented it by how I was clamping and assembling the project. If I had always assembled so I was working above the pocket hole, it would have helped. Obviously you can't do this joining side-to-side to create a large, flat piece of wood (or can you and I just haven't thought of that solution yet??!!), but for a join where it is possible, go for the above-the-pocket-hole orientation.
Maybe this is intuitive for others, but it wasn't for me. Just throwing that out there for other newbies to this whole process!