For the jointer, there are a few things to look at.
Make sure the tables and fence are all flat. Get a straight edge and lay it across each. Move it to cover the entire area at different angles to make sure that they're true. Use feeler gauges or a dial indicator for precision.
You also need to ensure your infeed and outfeed tables are parallel. Raise them above the cutter head and put a straight edge on the outfeed. Check for gaps in the infeed side with a dial indicator on the straight edge or feeler gauges. Do this across the surface of tables to make sure the planes are parallel and one side or end is not drooping on one table compared to the other.
Also check the blades on cutter head and ensure that all of them parallel to and level with the outfeed table. Lay a straight edge across the table and lower it until it makes contact with the cutter head/blade. With the machine unplugged, rotate the cutter head by hand to make sure your straight edge is exactly as the top of the cut. Use a dial indicator to check both sides of each blade to ensure they are all in line with the outfeed. Adjust the blades as necessary. You may need to look up a user manual for the procedure.
Once you know the tables and cutter head are good, check the fence and fine tune it to your square. Check it with feeler gauges. If it's tight to the square and still not producing 90* cuts, your square may be off. I use high precision machinist squares for setting my tools because the tolerances are super tight. A try square or combo square may be slightly off due to wear or, in the case of try squares with wooden bases, warpage and shrink/swell over time. Even digital angle finders are not super accurate. It's always good to remember that your tools are only as accurate as the tools you use to calibrate them, so never skimp there.
If you don't have machinist squares, flatten a face on a piece of hardwood and run it through a planer. Joint the edges on the jointer using the same face against the fence. Mark the face you used to joint the edges and rip the piece down the middle. Compare the jointed sides by laying both pieces on a flat surface and putting them together. They're should be no gaps. Flip one over and compare them again. There should still be no gap. If there is a gap, use the marked face to determine which direction your fence is out of square. Joint the edges again and go through the same process until you have no gaps.