tl;dr: if the PNR given is good for the airline website, you are good to.
This is difficult to assess. The problem is that "umbrella" PNRs exist for many legit purposes, consider these like a folder where you can have many individual trips with their own PNR. Often the booking agency won't let you know without some prodding (usually over the phone) the individual PNRs either -- your clue will be the fact you can't log into the airline website to see your trip with the PNR given. But the 3rd party website, checkmytrip and similar does show your trip.
So using such an "umbrella" the 3rd party is perfectly capable of creating two independent bookings. As they say, don't suppose malice where stupidity would do -- some crafty travel hacker software engineer who thought of grafting two trips together might have forgotten the MCT checks.
Because there's such a thing in the GDS, called Minimum Connection Time which is not accessible to the general public (grrr) but is often posted by insiders to various wikis, flyertalk, etc. So you need to Google (or ask here and we will Google for you, it's not like we know) the MCT for the given route. It will be like International-to-International at airport B or some such. If the booking is within the MCT then such hacking is unlikely and the airline doesn't sell you for whatever random reason and you should be good to go.
If the PNR given to you allows you signing in to the airline website showing the whole booking, you are good to go. If it doesn't and when calling the 3rd party customer service you are given two PNRs for the airline, you are in trouble. Merely having two PNRs for a complicated trip wouldn't be trouble, in fact it's quite normal but for a single trip with two legs on the same airline, that needs to be on the same PNR. (As an example, I was flying Amman-New York-Vancouver on Royal Jordanian and Cathay Pacific and you can book this with American Airlines over the phone and you will end up with an RJ, a CX and an AA PNR -- for whatever reason, none of the three will sell you this ticket online.)
If third party does offer booking within the MCT then I would screenshot it and ask them WTF are they doing and if the feign ignorance then send it to at least the airline but also, if USA based,
I would email firstname.lastname@example.org because I think the IATA would be quite interested in such a blatant rule violation.