Oh, it's definitely no trouble in use, just in nailing down what happens when they're treated differently and it feels to the speaker like they're treated the same. It's just trouble in analysis. For me anyway.
One of my favorite things to study is how sounds do or don't meld when they're slammed against each other. I like those stop + fricative sequences. :D

      From: Melroch <[log in to unmask]>
 To: [log in to unmask] 
 Sent: Monday, November 7, 2016 2:35 PM
 Subject: Re: Back to Phonology
There isn't any trouble at all. From a systemic viewpoint affricates *are*
"stops" in most languages which have them, so they are, still from a
systemic POV, not substituting one category for another when they have an
implosive stop paired with a pulmonic affricate. That's why phonology and
phonetics are different disciplines! If you like you can think of
affricates as a kind of stops with a really slow plosion phase. :-) It's
not totally facetious, since there are languages which contrast affricates
and stop+fricative sequences, e.g. Polish.


Den 7 nov 2016 20:31 skrev "The Scribbler" <
[log in to unmask]>:

> Thank you! It does sound like it could be analyzed as either for the
> purposes of explanation and I should probably stick with the one easier to
> notate, but glad to know I'm on the right track! It did make sense.
> This is the trouble that comes of speakers treating affricates and
> fricatives like stops. Though I'm looking into how languages treat their
> fricatives and stops differently and looks like there's other languages
> that have less voicing distinction on their fricatives than their stops, so
> I'm poking through some of those languages to figure out what gives.
> Thank you again for all the help! You're the best.
>      From: Melroch <[log in to unmask]>
>  To: [log in to unmask]
>  Sent: Monday, November 7, 2016 10:14 AM
>  Subject: Re: Back to Phonology
> That does indeed sound like a [d_j] (palatalized d) of some kind.
> Palatoalveolar and alveopalatal stops are also possible although so rare
> that the IPA (unlike some specialist transcription systems) doesn't have
> any distinct symbols for them. A fricative becoming implosive is however
> just the situation where I'd expect them to arise.
> /bpj
> I hope this makes sense. I'm writing with my daughter's 2yo leaning on my
> chest while watching cartoons on my phone! :-)
> Den 7 nov 2016 16:37 skrev "The Scribbler" <
> [log in to unmask]>:
> > On Question 1. Could it be a palatalized alveolar implosive stop? I'm
> > basically using the same point of articulation as the implosive d, but it
> > seems distinctly palatalized and sounds like a nice cross between j and y
> > (which is horrible analysis, pardon my American English ears). In short,
> if
> > I was making it off the palate, I probably would just analyze it as J\,
> but
> > I'm not actually making it off the hard palate.
> > Are palatalized implosives a thing? Okay, besides b. And if yes, could
> > that feasibly stand in for an implosive j affricate, substituting a
> > palatalized alveolar implosive? Which would also contrast with the
> > nonpalatalized.
> >
> >
> >
> >      From: Alex Fink <[log in to unmask]>
> >  To: [log in to unmask]
> >  Sent: Thursday, November 3, 2016 11:14 AM
> >  Subject: Re: Back to Phonology
> >
> > On Thu, 3 Nov 2016 15:35:27 +0000, The Scribbler <
> > [log in to unmask]> wrote:
> >
> > >Thank you, everyone, for all the help. I've got a couple more questions
> > based on my homework. :)
> > >
> > >Question 1. In doing further study on affricates, fricatives, etc., I
> ran
> > into the idea that the implosive palato-alveolar affricate is not a
> thing,
> > but I don't have any difficulty saying ja implosivized the same way I say
> > ba. Am I imagining things? Is this safe to include in my conlang with an
> > implosive series?
> >
> > Up to you.  But what nature seems to say is this: they may well be
> > possible, there are scattered reports of them, but they're unquestionably
> > dispreferred.  Usually one finds that a language with palato-alveolar
> > affricates and an implosive series will have a palatal implosive stop
> > instead, or occasionally some other sort of substitute like /j?)/, or of
> > course just a gap.
> >
> > I assume the acoustic motivation for this is that it's very typical for
> > implosives to have _no_ flow of air either in or out when the stop
> closure
> > is released, vs. pulmonic stops which have a burst of air escaping.  If
> > there's no flow of air then it doesn't matter if you immediately put your
> > tongue into position for a fricative: the noise of fricatives comes from
> > the turbulence of air flowing through a narrowed passage in the mouth, so
> > no flow, no noise.  Can you hear a difference between your implosive "ja"
> > and [J\_<a]?
> >
> > >Question 2. When it comes to minimal contrast pairs, I have allophones
> in
> > complementary distribution for various stressed positions, but stress
> > itself is phonemic, changing the meaning of the word. In a situation
> where
> > a'shi means something different than ashi', would the allophone for
> > stressed a be phonemically contrastive with the unstressed a or would
> they
> > both fall under a in the phonemic inventory and be treated as allophones
> in
> > the phonetic inventory?
> > >
> > >I was doing the latter and treating stressed allophones as just that,
> but
> > considering there is a semantic difference when stress is applied to a
> > syllable, does that make it a minimal contrast pair and mean I should
> > consider them separate phonemes? That always confuses me a bit.
> >
> > AFAICT you can still get away with analysing stress as contrastive, and
> > the difference between e.g. stressed and unstressed /a/ as allophonic.
> The
> > minimal pair in your last paragraph would be a minimal pair *for the
> > position of stress*, not for a contrast between segments.  Suprasegmental
> > phonemic contrasts are a thing: is the source of your confusion that you
> > are (implicitly) assuming that all phonemic contrasts have to be in
> > segments?
> >
> >
> > Alex
> >
> >
> >
> >