As long as the higher salaries are based on a business necessity and are done in a non-discriminatory manner and/or have an impact on protected groups this would not be a problem under EO11246. Remember that OFCCP is not the "pay police" but tasked to evaluate compensation to ensure that it is administered in a non-discriminatory manner. As for the compensation directive, if you have a very small workforce it may not be possible to put together groups of employees that are similarly situated and have enough in a group to conduct a meaningful regression analysis. There are other statistical tests like Rank Sum, Fishers Exact, etc. that can be used for small groups.
You can use this OFCCP audit checklist to ensure you're doing what is required to maintain OFCCP's regulations including VEVRAA, Section 503, and EO 11246. Or request a demo to streamline your compliance and recruiting efforts.