First this isn't related to my App, so maybe not the best place to post. My tool is used to create TOC automatically.
Second, because of the way eReader works, a page on a iPhone or on a Kobo will not be the same, also depends on the formatting you have done. So most reader just calculate the page number (I think 1000 word is a page) or like iBooks it just has a page number for each page, so if you put the fonts bigger, your number of pages will increase.
Because of this there is some reader that put the "real page number" beside the calculated page number (the Kindle I think does this), but it must be written inside the TOC. I do not know what you have done, but my thought is that it is these page numbers you have stated, which is very optional.
Also not knowing for which application you are trying it I can't tell you exactly why you are having this problem. I suggest that you read the ePub Specs for all the information you need and more. Also use software like Sigil and calibre, if my tool can help you give me some feedback.
You must mostly need the navmap part of the TOC, if you have anything else, just ignore it.
NCX Specs
Info on Page Numbers in TOC