I believe this is something the enumerator took upon himself to do, noting something other than escaped slaves. The first 8 pages of Lincoln County are dated August 5-8 by assistant Marshall Jno W Shelly. No marks are made next to Mullatos at all and he identified one as albino on page 1. (There are a few dots or very small marks on page 2) Then on the 9th image, August 26, the census for this county was taken over by Assistant Marshall L B Taylor and the check marks begin in ernest. But the handwriting all looks the same and the dates jump all over. Also some pages further in have Shelly's name on them and have markings. I've never notice dates amd page numbers not being consecutive or more than one name before. I'm thinking one of the men must have copied the other's work because it looks like all the same handrwriting. If the pages were loose leaves, they were compiled wrong. I went to the last page, hoping to find a clue about these check marks but no clue. As a side note, the numbers at the bottom of the page are the number of male and female in that column.
I took a look at the Muhlenberg, Kentucky Slave Schedule for 1860 because someone at History Hub mentioned seeing the same in those county records but the enumerator was doing some kind of numbering, not marks. Mulatto males and females were counted separately. When the number reached 100, the enumerator started over again. See for yourself. This is clearly something the assistant Marshall took upon themselves, perhaps ordered to do so behind the scenes. In that year, there were lines for totals at the bottom and the escaped slave line was blank on every page for that county.
Given the fact that Kentucky had oulawed importing slaves for some time, had a large slave market, and was known as a breeding state, they might have wanted to know how much breeding was going on by the owner, his sons or the task masters. There was no way provided on the census form to separate the numbers of each, only of male and female in general. Perhaps Taylor was counting but not numbering and reporting that number verbally to someone.