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Are you talking about the ridge created in round 8? If yes, you're supposed to have a ridge on the inside of the cup after round 8. You'll use the ridge to make the coffee lid.
When you crochet into the top of a stitch, which is inserting your hook under both the front loop and back loop, there is no ridge. When instructions say to crochet into the front loop only (FLO) or back loop only (BLO), it creates a ridge. Your pattern is crochet into the front loop only in round 8. When you do round 9, you'll crocheting into the back loop of round 7. This is the loop that you didn't use in round 8. When you do this, the ridge inside the cup will disappear.
Does this answer your question?
After typing all of this I took a look at the pic in your first link again. I didn't realize that it was a pic of your work in progress when I first looked at it. Are you talking about the bumps along the side?
Most amigurumi is done in a spiral, where you keeping going at the end of each round, instead of finishing a round and starting a new one. This pattern isn't done in a spiral. When you join, it's with a slip stitch to the top of the first SC stitch. It looks like your join might have been to the chain 1. You have to ignore the chain 1 when you do your slip stitch join. When you go around, you have to be careful that you don't crochet into the the slip stitch. Both the chain 1 and the slip stitch don't count as stitches. Count the number of SC stitches around. Every round from 1-8 should have 10 SC stitches. If you have more than 10, then you're crocheting into the join or the chain 1.
One thing you can do to help see where the first SC is on each round is to use a running stitch marker. Get a piece of scrap yarn in a contrasting color, about 6" long. (Note: the exact length isn't important.) As you start round 2, lay the tail of the scrap yarn across round 1's first SC, with the short end sticking out towards you. Capture the scrap yarn under round 2's first SC stitch. Before you start round 3, flip the scrap yarn towards you. Capture the scrap yarn under round 3's first SC stitch. Continue flipping it back and forth under the first SC stitch of each round. When you're done with the project, pull it out.
I use a running stitch marker for all rounds that are going to curl (e.g. amigurumi, hats, bowls, etc..) Running stitch markers are great for seeing where the rounds begin and making sure that your first stitch in each round is in the right place. Because crochet stitches lean, the running stitch marker will spiral to the right slightly. This is normal. It's also handy for counting how many rounds you've done.
I hope this helps and those bumps disappear for you! Let us know either way. Also, please post a pic of the finished coffee cup. It's really cute!. You can post pictures in here by using the Attach Files section, located underneath the box where you type your post. If you're replying to a post, you have to click on More Reply Options in order to see the Attach Files section.