Upfront fees are a HUGE red flag.

Of course there is no strong reason not to use a QC deed but it is a red flag. 

If one applicant has an 800 score and the other applicant has a 500, there is still a good chance both will be approved.With that said, this scenario is different and it does not seem to be a red flag as some individuals don't take out any credit at all for one reason or another.

Are there any red flags that I should watch out for in selling a property via seller financing to a trust as opposed to an individual? 

Does this throw any red flags?

While transferring the property into the LLC can trigger the Due on Sale Clause, transferring properties into a Land Trust does not trigger the same red flags from a bank. from there you can nest the Land Trust into an LLC, still granting you the liability protection of the LLC.

If you ask for too much info up front, it raises some red flags.

The reason we waited is that when the loans are sold, analysts will review the loan details and may notice that the mortgagor and title hold are different (if you've already transferred to an LLC) which can cause the loans not to be sold/purchased and become a flag that causes the loan to be called due. 

I've found that it's a red flag for future trouble.

Also, it was recommended to not have words such as "property", "investments", "real estate..." etc in your LLC name, as it can be/is a red flag to lenders and can make it a challenge to get lending.