Greatings estreya,
I'm not near as knowledgable on Mason Orchard Bees as perhaps I could/should be; however I have maintained the wood block style "home" around my house for the past many years. I would offer up this observation, first the darker coloured mud plug doesn't necessarily mean a different species of bee - probably just means the dirt around your home is different than what they have, where you bought your bees from.

Also, the term 'Mason bee' is fairly widely used and a quick search on the internet will reveal this label can (and is) used to describe bees of varying colour; from greenish to blueish to almost blackish.

Maybe the newest generation of bees you're seeing are from 'indigenous' (gotta love that term...even, if used, on a local regional scale!) bees. However, if the reason you got Mason bees to begin with, was for pollination purposes, I'd say let the indigenous bees make themselves at home - you're still serving the same end result, right?

But also some wasps can make themselves at home in your cardboard tubes and they are MUCH less efficient pollinators than Mason bees - so I'd be more on the lookout for them. Look for very smooth mud cap plugs that the wasps build - roughly finished mud cap plugs are the Mason bees.

It appears from the photo that your tubes have the paper inserts used to help keep the tubes clean (clean holes being much prefered by female Mason bees). That also allows for the ease of refrigerated storage - which you may want to consider. I, personally, DON'T do this - I simply leave them alone and let Mother Nature take it's course. I do clean the holes out from time-to-time however. This is one topic you need to reasearch yourself and come to your own decision about. My sense is, in your part of the country, there is a tendency to use the refrigeration technique. Perhaps someone else will enlighten us and point to the error of my ways... feel free to comment all you Mason Bee experts!

Your local mud is darker than the location where the original plug was bought from. That's all.