1. Poor choice of contrasting colors
So you have a logo that's dark red, don't choose a dark background. If your logo is a light yellow don't choose a white background. Color contrast is so important on a step and repeat banner but so commonly overlooked.
2. Logo's are too big without enough white space
The biggest logo doesn't win. The purpose of the step and repeat is to provide subtle branding, people aren't going to want to share the photo's they take in front of your backdrop if it's cluttered with over sized obnoxious logo's.
3. To many logo's with too many colors
If you have too many logos and the step and repeat starts to look like a Christmas tree try switching to a B&W design. The increased color contrast will make it look a lot classier.
4. Aspect ratios of logo's don't match
You have two choices here, shrink the larger logo so it looks proportionally spaced, this will give the step and repeat a lot white space and can look strange. Add something like the company name or URL to the square logo so it matches the aspect ratio of the other logo's.
5. Low quality JPG logo's from websites
As graphic designers we know better then to just grab any image of the web and try to print it but at least once a week I receive a step and repeat design with a logo that's been enlarged +500%. It's not going to work, I promise you it will print crappy, look crappy and the whole point of a step and repeat is to represent your brand! If for some reason you can't get a high quality logo try using text instead or adding a FB link?