This looks like a bug. I can reproduce it in FM7.1/Unix.
It fails on superscripts as well, and probably any Character Format applied to a paragraph picked up for TOC.
The TOC entry is working hypertext right up to the subscripted character, but nothing beyond that is.
Using a variable for the subscript doesn't help, either.
Possible work-around:
You might try using \u2082 (Unicode native subscripted 2) if that code point is populated in your font. I can't test that, as FM7.1 doesn't do Unicode.
Looking at the MIF generated was no help.
The <MTypeName `Hypertext'> tag actually ends > # end of Marker before any TOC <String begins.
Frame must be using internal rules to render each TOC line as hypertext in the PostScript.
I didn't study any Ps output because it's even less comprehensible.
When no subscript is present (normal TOC entry), there are two <String instances per line; one for the paratext and one for the page number.
When a subscript is present, each line contains three or more <String instances.
My rough guess would be that FM's internal illogic is getting confused by more than 2 <Strings.