Jan,
I worked on a project of my daughter and the pattern called for 287 5.5" squares. I did get in a rush and stacked the fabric to make the half square triangles so they did come out uneven. Long story short, I got a 4.5" square ruler, squared them off and put them together. The ones that didn't square up to 4.5", I set aside, I ended up putting 50 of them aside, so chances are your project can still be "saved".
In my MOST HUMBLE opinion, if they match up or not, the time and effort put into it is worth every stitch upon completion. I haven't been sewing very long myself but I've noticed improvement after moving on to the next project.
Happy Sewing/Quilting Jan!
Monique