Personally, "your" and "you're" are not homophonic. Without delving into the subtleties of IPA, as it applies to my accent (and those I most frequently encounter) the former is more a homophone of "yaw" and the latter like a truncated "urea".
The three th* words are much closer, I'll admit, but in comparing "there" and "their", there's a certain oral constriction (*fnar fnar*) for the latter that isn't present in the former. The third in the series has a (different) squeeze
and gains an extra syllable... no, not
quite (i.e. my version definitely isn't as pronounced as if I were from the American Deep South), and maybe it's a
half-syllable if that's possible. But it definitely heads towards "they'ur". (Noting as a reference that I'm not given to extending words like "film" (Northern Irish: "fillum") or "vehicle" (especially US deep south law enforcement style "vee-HICK-әl", but neither do I tend to glottalstop or use the "reverse cockney L"[3]. In polite company, at least. I'm very close to a geosocial divide where "th"s turn into "d"s, though, and might sometimes lapse thusly.)
Not that I'm saying that my personal rules are going to be universal enough across the whole English-speaking world to
correctly hear these subtle differences in others but, for most people I would interact with daily, they're there in their speech. Interestingly
spoken correctly (at least, never jarringly wrong), but when it comes to written text one cannot really be ambiguous enough to slip under the radar on that point.
OTOH, the "Could've"=>"Could of" confusion[1] I
attribute to a homophonic conjunction having occurred, as (for want of a better set of stereotypes to blame) the inner-city inter-cultural mix of accents bring the "әv" of "'ve" towards the "ov" of... well, "of". And hearing "ov" enough it gets engrained[4] in spelling as well. Still, absolutely hate hearing it. (OTOH, when I
expect it from a character in a film or drama, it'll jar when they
don't use it. Still can't stand it from 'real' people. And there's no excuse for writing it[2] and I restrain myself (
most of the time) when I see it here to not send an advisory PM. And I hate it when I
do succumb to temptation, with the flimsy excuse of saying something else at the time. No excuses and no apologies, though, but I regret most that I
have to do it.)
But that's me and my thoughts, and doubtless none of this travels
quite so well as I might imagine.
[1] A generous word. Personally I think it's as heinous as pronouncing "ask" as "aks/axe"
[2] "Language changes" be blowed. It transitions and evolves, yes, and there are novel idioms developed (even mondigreens), but this is like a colony of moles developing flight.
[3] "Milk" => "Miyuwk"? No, I don't know what IPA would do with that, either. If you know it, you know what I mean.
[4] Or, if you prefer
ingrained. But the above alternate is how I say it (with both spellings being valid), while we're on the subject.