You are fortunate it was low enough to retrieve. One of my sons has been storing one of his drones about 200 ft up in a tree for the last few years. The return to home altitude was not set high enough to clear the trees.
I have definitely had birds attack my quadcopters dozens of times (over about 15 years of flying).
The easy ones are actively nesting birds, like swallow, kites, and some sea birds, but they give up easily when I fly away from their nests...
You know, you might be right. These guys must be getting permits because no one would break the law in a dozen ways like this. O who knows, under the new administration, perhaps the new NYC mayor suspended the old drone permit program so now...
Firmware updates have always been something of a mixed bag - sometimes adding useful new features, but more often than not, changing things, and restricting more things either at the time or later. For that reason I am unbothered if these updates...