You can sometimes get away with angled cuts on a scroll saw but in the majority of projects, a perfect 90 degree angle is critical. There are a variety of factors that can lead to angled cuts. Some of them can be a quick fix and others will make you tear your hair out. Hopefully after reading this post, angled cuts will be a problem of the past.
1. This may seem obvious but the first thing that you should always check is if the blade is 90 degrees to the table. Even if you set the table at 90 degrees earlier in the week, there is always a chance that it somehow shifted. Leaning or pressing your hand down on the surface can tilt the table a fraction of a degree which can make all the difference. A quick and easy way to check if the blade is a perfect 90 degrees is to take a small piece of scrap wood and make a shallow cut. Turn the saw off and spin the scrap piece of wood around and try to feed the blade backwards into the kerf line. If the blade slides in perfectly, you're all set.
2. Blade tension or really lack there of can be a factor. A blade with too little tension will bow often in the middle creating a cup shaped angled cut. If you notice this, do a few test cuts and increase the tension to see if the angled cut reduces or goes away. Blade tension can be a difficult thing to master and usually needs small adjustments for different types and sizes of blades. Some advice that's given in the scrolling community is when you pluck the blade, if you hear a sharp C note, its tension is correct. If you're anything like me, figuring out what a C note sounds like is like figuring out theoretical physics. I do pluck the blade and listen to the sound but I'm clueless if it's a C note. Practice is the best solution for proper blade tension.
3. Improper blade selection can sometimes result in an angled cut. For instance, If you try to cut a 3/4" piece of purpleheart (a very dense wood) with a number 1 reverse blade, your going to have a difficult time getting cuts without an angle (not mention a good chance of charred wood and a pile of broken blades). The thickness and hardness of the wood are big factors in blade size. In general, we use 3/4" to 7"8 wood for everything we make and I alternate between a #5 and a #7 blade. For very dense woods such as yellowheart, use a #7 blade. Lesser density woods such as American cherry, use a #5 blade. Wood less than 1/2" thick, use a #3 or a #1 blade. Wood thicker than 1" will often create a whole mess of issues. It the cuts are not very intricate, use a #9 blade (This blade is fairly thick and doesn't take kindly to tight curves.)