I have tried to submit cis return direct from quickbooks to hmrc and it has been rejected?

Thanks for submitting your first post here in the Community, @splaceyroofing. I'm here to share insight on filing CIS in QuickBooks Online. 

Beginning the 28th of September, you can only file directly to HMRC if this is an earlier CIS returns. Otherwise, ensure your credentials are correct before filing it directly from QuickBooks to avoid rejection. Here's how :

1. Go to the Gear icon, then select Accounts and Settings.
2. Go to the Advanced tab and expand the CIS settings by selecting the Construction Industry Scheme (CIS) option.
3. Verify your UTR no., Employer’s PAYE reference no., and Accounts office reference no.

Then, follow the steps to file CIS returns in QuickBooks Online. 

However, if you are still unable to continue, I'd recommend contacting our Customer Support team. They can check your account to see why it's rejected and help you resolve the issue. 

Just in case, you'll want to read through this article to help you learn about recording Deductions Suffered under CIS and submit the figures to HMRC.

Know that I'm always here to provide my utmost support should you need more help at any time.