I don't have any deep insights, but will follow along since I have purchased the Mohawk stain/dye to use on on the floorboards and thwart of my Lake Union Swift build. 

How long was it between applying the dye and applying the epoxy?  And what was the approx. percentage of added denatured alcohol in the dye mix?  What were the ambient temperatures?  Obviously I'm wondering if the alcohol hadn't entirely evaporated, although I would expect it to pretty quickly.

For those not familiar with it, CLC sells the Mohawk stain/dye product, and their descriptions starts with, "This dye-type stain is ideal for projects that will eventually be sealed with epoxy (stain must be applied prior to epoxy coating)."  

Speculations:

  ...a second coat of epoxy...

So you dyed the items after they'd had a first coat of epoxy? Maybe not a good idea if the dye somehow acts as a release agent.

...I did sand up to 200 grit.

The raw wood parts before their first coat of epoxy? Did you also then do your best to remove any remaining sanding dust?

Usually a coat of epoxy will saturate whatever dust that's left on wood surfaces after sanding, but if there's too much it may inhibit a proper bond. After all we use wood dust (flour) as epoxy thickener. If instead you mean you sanded before staining, that's the proper approach.

Or perhaps you meant you sanded your first coat of epoxy then applied the stain?

Alcohol tends to lower surface temperatures when it's applied to something as it takes heat away during evaporation. This can lead to ambient humidity condensing at the surface, which takes longer to evaporate than alcohol depending on both ambient temperature as well as humidity. If the latter's relatively high for the temperature, it can take quite awhile to leave. Obviously applying epoxy to a surface that's contaminated with condensed water vapor isn't optimal.

You've been using the same epoxy components with success up until this incident? You mention that This is an issue ive only experienced on dyed parts so I'm wondering if you perhaps have a batch of dye that's improperly compounded? Or your alcohol's contaminated somehow?

Not knowing where you're doing your building, I can't know just what kind of alcohol you're using. Different countries have different regulations about what gets sold as 'alcohol'. Here in the US we have 'denatured alcohol' which is most commonly ethanol (same stuff sold as an intoxicant when suitably flavored and diluted) that's been tainted with methyl alcohol to render it undrinkable (and thus not subject to taxation as liquor) which is toxic.

Other countries sell different products labeled as 'alcohol' so perhaps what you're using for mixing your stain has something else in it that's causing epoxy adhesion to be less than what you expect?

Again, all speculations until we can learn more about what you're using and maybe your methods.

   I've epoxied over a lot of mohawk alcohol based dye and never had an issue. I've also mixed the dye right into the epoxy to make matching fillets. I do not think the issue is your dye.  I think you either have a surface contamination issue, or your epoxy mix is off. Are you weighing your mix or using the pumps?  The pumps that came with my MAS epoxy were garbage. I switched to measuring by weight, it's faster and more accurate in my experience.

I think you either have a surface contamination issue...

Be my guess, in light of the comment:

...a small airpocket that wasnt there beforehand and upon sceatching with fingernail it got larger and larger. Not to the point of flaking...

The epoxy's tough enough to withstand the fingernail but the bond between it and what went down before is suspect.

...or your epoxy mix is off.

Still, if it's not sticky after 24 hours and can't be scraped away with a fingernail, and able to withstand being pulled away in sheets, I'm less cioncerned with proportioning.

I've used the CLC-supplied pumps for years now for 99.9% of my use of MAS LV product, have yet to experience a bad mix (fingers & toes crossed as I type that). But my pumps aren't your pumps or the OP's, so maybe... yet I go back to the phrase Not to the point of flaking.

If the instance the OP's posted about isn't their first:

This is an issue ive only experienced on dyed parts.

My focus would be on how stain is being mixed, applied, then what gets done to the stained parts before epoxy's laid on top.

Lastly, 200 grit I think is too fine for pre-finish work with epoxy. 100 to 120 grit ought to serve just fine at that stage, save the 150-180-220 for final sanding of epoxy / varnish / paint before last topcoat.

Finer than 150 grit, used on parts before epoxy application, may leave too little 'tooth'; there's such a thing "as too smooth."