My first thought, without delving any further, is that you could be looking at two different baptisms. The John Marshall (fathers) could be cousins for example.
The occupation and place name and dates of baptism are different, so enough differences to point towards there being two families.
Have you checked the 1841 census to see if you can find two families with father John, mother Ann and son Thomas in the same kind of area?
I have, but the findings only muddy the water more. There only seems to be one John and Ann together in Leeds. On the plus side they're in Meanwood, which is one of the two places listed on the baptism records; and John's occupation is Delver, which
http://rmhh.co.uk/occup/d.html says is a stone quarry worker. On the negative side though, they have six kids with them and none of them are Thomas.
Looking at Thomas's of an appropriate age, I get four. First two are probably not applicable (one with a William & Hannah of parental age, the other with a Francis & Hannah). The third is in the right place again, Meanwood, and there's an Ann there but no John. Ann is described as a stone merchant, but is in the 60-64 age range which is borderline for them to be mother and son, she would've had to have been in her late 40s. The last is at Trafalgar Street Academy with other kids, a couple of teachers and schoolmaster. No idea who his parents are, they could be the John and Ann from earlier, but there'd be a question as to why he's at school and the rest are home.
The reason I came across the two Thomas's born on the same day anomaly is because I was looking for potential siblings for Hannah Marshall born in 1811. Chapel Allerton register had her parents as John Marshall and Ann Wood from Woodside, but no father's occupations seem to have been listed in that period. Hannah's second marriage certificate says her father was a Delver which would point to the John from the 1841 census, but he and especially his wife are way too young (40-44 and 35-39) even if they could still be Thomas's parents. The Ann on her own may be her mother, but then that would mean there *are* two sets of John and Ann kicking around the same parish. Which if that is the case, then I've found a good half dozen baptisms in Chapel Allerton registers which could be attributed to either of them. Most of the time, labourer John is in Meanwood and quarryman John in Woodside, which would seem to present a clear difference to work with. However one of the baptisms in 1816 has quarryman John in Meanwood just to make things complicated again.
Update (5:03am): Oh, and just to make things even more scrambled, I've found a place west of Chapel Allerton on the 1851 OS map called Meanwood Side. A few decades earlier, could that have went by Woodside?
Update (12:51pm): I've looked at the 1851 census. Of John & Ann's family from 1841, two of the kids are still at home, plus one more born since the census, *and* now Thomas age 23. His occupation is down as Labourer in Stone. Ann is now a widow age 49. Could this be the Thomas who was at the Academy 10 years previous? Or could it be the Thomas who was with the 60+ Ann in 1841 and she's the grandmother? Unfortunately none of the other Thomas's in 1851 have a birthplace which matches up.
Update (1:27pm): And it gets weirder. Looking up John Marshall to see if I could define labourer John and quarryman John as two people or the same person, I found the following in The Leeds Times, either of whom could be the husband of the 60+ year old Ann.
2 May 1835: Inquest at Meanwood on the body of John Marshall, 61, who died in an accident at a quarry when "a quantity of earth fell upon him", injuring him to the point where he died "shortly after".
20 May 1837: Inquest at Chapeltown on the body of John Marshall, 64, who died in an accident at a quarry when "the upper part of the perpendicular height gave way and buried him". He was dug out but died 15 minutes later.
