So, let's say that one of the lost SCP is turned out to be owned by MC&D, maybe after CI sold it to fund their actions. Or maybe a possible skip was lost during their recovery and a few months later it suddenly appears on the catalogue of MC&D, would the Foundation rather to go and raid their warehouse or would the Foundation attempt to buy it?
I'd think it depends on what the item is.
There's a lot of Realpolitik involved in what the Foundation does, so I imagine they do hit up the MC&D auctions.
In the case of lower-level anomalous items, while they'd rather have it in containment, the Foundation will at least sleep a little easier knowing that the "unique vintage combustion ray" went to the collector of anomalous weaponry who just likes to blow up Priuses on his private blast range and not the third world dictator.
Even for the more dangerous stuff, at the end of the day, it's just plain less dangerous and cheaper to outbid everybody else for most of the stuff worth containing. I also kind of imagine that when the scary librarian lady representing Standard Component Productions starts bidding on something, you're going to think really hard about how badly you really want that memetic painting… and maybe wonder what's wrong with it.1
I personally headcanon full-on raids on MC&D being fairly rare, reserved mostly for the stuff that lies midway between SCP-1808 (picked up as a side-grab during a raid, but not the target of said raid) and SCP-2501, where even MC&D just goes "Um…here. You…you can just have this one".
Cue plug for MTF Mu-3 "Highest Bidders"!
The 'Operation: Free Market' story is all about how SCP-2463 was recovered in a raid on an MC&D warehouse. Mu-3 are a task force designed specifically to take anomalies from MC&D.
A lot of their work is in simply keeping track of MC&D assets; and it is simpler, when possible, to just buy items than steal them. But if getting secret intel and carrying out undercover ops are required, the Foundation can do it.