It sounds like you're purling using the "Combined Knitting Method" of purling (see "Basic Techniques/Purling"). This will result in a twisted stitch on the following knit row.
A lot of people purl this way; it's nice and fast. But you need to know how to untwist the stitch (and sometimes the following stitch as well), before working certain instructions.
To untwist a stitch, turn it clockwise and place it back on the left needle, so that the back loop is now in the front, and the front loop is now in the back. If you turn it the right way, it will not appear twisted. The front loop will connect to the knitting you've done, and the back loop will connect to the upcoming stitches. (Maybe I'll ad a video on untwisting a stitch...as soon as the clouds clear out here, and I can shoot!)
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