At the elite levels, deep sidespin and topspin serves mostly get looped, and are mostly used as occasional variations. But at lower levels they are often the bane of players who hit or loop them off the end over and over. Why do they do this? There are three main reasons.
First, they do not adjust to the amount of spin on the ball. A ball with topspin or sidespin is going to jump off your paddle faster than a ball that is not spinning, and you have to take that into account. If you don't, the ball will take off faster (and higher against a topspin) than expected, and so go off the end. So you must aim lower. (Note that while sidespin pulls the ball sideways, players who hit or loop the serve don't usually miss against these serves by going off the side since the spin takes less on their paddle when they attack the ball, and so it'll only go a few inches more to the side than expected.)
Second, they do not take into account that their contact point is usually closer to the table than in a rally. This is especially true for loopers. For example, against a block, a player may loop from several feet behind the table. But against a topspin or sidespin serve, the contact point is generally 1-3 feet closer to the table. This means that the far end of the table is 1-3 feet closer to you, and so you must aim lower or you will go off the end.
Third, they lift breaking sidespin serves off the end. This is especially true against ones that break away from the player. The reason is that they may hold his racket at the perfect height to return the serve - but then see the ball breaking away, and reach for it. When reaching, players generally lower their racket - and so they lift more, and go off the end. So make sure to keep your racket at the height you want to start the stroke - but even more important, learn to read the break of the serve so you don't have to make last-second lunges.
A solution to all three of these problems is to contact the ball more on top of the ball, especially when looping. There should be little lift.
How can you overcome these and other bad habits in returning these and other serves? PRACTICE!!! Instead of just practicing rally shots all the time, you and your partner should take turns serving to each other. You could play out the point, but it's even better to just get a bucket of balls and one player serves over and over while the other just receives. The server doesn't play the point out; as soon as he serves, he reaches for the next ball to serve. This gives you a lot more receive practice per time then playing out the point. Have the server give you the same serve over and over until you are comfortable with it, and then move on to another. When you are fairly comfortable against most of the serves you may face, then have the server vary them so you learn to adjust to each one. And remember - you don't have to kill or loop kill the serve. When returning serves, consistency, control, depth, and placement are king.