jallen has basically hit the bullseye here. This is almost always caused by one drawing having different properties than the project. Take a look to verify that assumption, but it's definitely the most likely cause.
And, regardless of how the dots were created, there's only one way to get them all the same size and that means changing the scale on the ones that are too big. Luckily there's a fast way to fix that.
After you've applied the project defaults to all drawings, you can use the Swap/Update Block tool to force all the existing dots to come in at a specific scale. It's hard to say what it should be for you. You can find out by clicking on any dot of the correct size and looking at it in PROPERTIES. Whatever its scale is, use that value and force all the other dots to be that same value. This will allow you to quickly fix all the dots in the whole project.
That being said, nothing here addresses the cause of the problem. How did some drawings come to have different settings from the project? Until that's discovered, the problem may reappear. (Assuming, of course, that jallen and I are right about the drawing properties lol.)

Jim Seefeldt
Electrical Engineering Technician