If you have a page with the following items
<p id="t1">...</p>
<p id="t2">...</p>
<p id="t3">...</p>
<p id="t4">...</p>
Then a link to any of those targets will produce the same displayed page. This may change if you increase the font size so much that the later elements get shuffled off onto the next page or if the ToC is long enough to stretch over several pages. The use of a fragment merely ensures that the result of a link will display the page in the file that contains the target to which it refers. If you omit the fragment identifier then the link will always point to the first page in the file.
I don't know why you're having this problem, but it sounds like a problem with the settings you use for conversion, or maybe a bug in calibre.