There's three answers here that are all in part correct. Firstly Raynor says that Tolkien included characters such as Tom to add 'depth', then Boro says it was due to Tolkien having less time to devote to his work, and finally there is Esty's answer that it all adds mystery.
Tolkien did indeed have less and less time to his work as he grew older. Remember he was an academic with a large family, and was not a high earner. From reading the new Companion & Guide I've been horrified to learn just how hard he did work in his middle age just to keep his family fed, clothed and housed. He was on a relatively low wage and had to accept all kinds of work external to his University work, including marking school exam papers and even civil service entrance exam papers. He was on a multitude of committees, and took a full part in the life of Oxford, even acting the part of Chaucer in the Summer revels, and was a fully active 'family man', doing DIY and all the rest of it. Most of Lord of the Rings was written in the early hours of the night.
Even after retirement he found little time for writing, he had the business side of being a writer to deal with, including answering countless letters, and his health was not good, nor was Edith's. Middle-earth often came very low down on his list of priorities and this seems to have been a source of great frustration. If he did leave things such as Tom in accidentally as inconsistencies then I'm surprised there aren't in fact more and its testament to his meticulousness.
But characters such as Tom also add in depth as Raynor has brought up. Any real mythology has odd instances such as Tom or Ungoliant. Step inside Middle-earth for a moment and only Eru knows why they are there. The rough and fuzzy edges are what separate Tolkien from his vastly inferior imitators who wish to have everything 'categorised' and neatly put into boxes like Art is just some dreary dull 'science' or computer programme. The urge to put everything in Tolkien's work into defined sections is no better than the urge to file documents. I like to think Tolkien did it on
purpose just to fox us all and stop us doing exactly that kind of thing. You cannot do this with the real world, and you cannot do it in Tolkien's world.
Never will be able to either, as he is now gone.
Finally as Esty says, do we really want it all to be neatly squared off anyway? How
boring would it all be then?! Mystery is beautiful...