For the most part, regular thread in the bobbin will make the back bulky but other than that shouldn't cause any real problems.
Do you mean you put matching colored thread on top and bottom of items you sew. I don't think I have ever done that except for things that will show on both sides. I always use white or black. I luv the prewound bobbins and use them the most
as long as the pattern came out ok should be no problem. You can use the top thread on the bobbin if you want the same color on bottom and top. Just shouldn't use bobbin thread on top for some reason. Anyway I'm sure it's fine. I use top threads on bottom often. *4U