Can calling wp-blog-header on a static page hurt google seo rankings?

My company has been setting up wordpress blog’s for existing websites and then calling the wp-blog-header.php file to then show 3 recent posts on the original existing static php (non-wordpress) homepage.

Everything worked perfectly but then after a while a client’s website got flagged on google for some reason. All the code and links are clean, no black cat stuff, no hacks, so we decided to remove the wp-blog-header call and then the flag went away.

I’m not sure if this was coincidence or not but I’m assuming not, I just wanted other people’s opinions on whether or not this can happen because we’ve done it to numerous websites. I’m also wondering if it’s the theme we used as well (same one for all sites: blaskan — free theme so maybe it’s an easily hackable one?)

Any advice would be greatly appreciated.