I think they legit tried to resign him, and were taken by surprise by the SD offer, as apparently all of baseball was.
Body language reveals a lot, Bloom was bragging about big things happening that day and after Bogaerts signed he had a look on his face like his entire family just perished in a plane crash.
Don't want to rehash this, it's been debated almost as much as Mookie on here, but some would come in and say the Sox botched the Bogaerts situation by not extending him further before he got to free agency, and I would be inclined to agree.