So Boston had JJJ on the block (3.5/4.0) and I offered a young SF (3.0/3.0), and young C (3.0/3.0) some and another young PG (2.5/3.0) plus TWO first round picks and they still wouldn't take the deal. Then towards the trade deadline, they took a deal for some scrub and one first. Is there any reason that they took a much lesser offer? I tried multiple times throughout the season to try to trade with them, why would they take such an offer that had much less? Is there something I'm not understanding or is that just the way it is?

Well there's a ton of factors that could play in play here without looking at your game I can only make guesses but here are some possibilities.

1. Maybe there was a problem with JJJ where his attitude towards the organization had plummeted and they knew they had to trade him and that was the best offer they could get at the deadline.
2. You didn't say anything about your team. Who were the players you were trying to trade? Did they have big contracts that Boston didn't want? Were they about to come off a rookie contract and Boston didn't want to pay them? What else was it you were looking for because I'm assuming if you were trading 3 players that you must have been getting some other kind of salary back. Were you a good team? A late first round pick really isn't worth that much in the grand scheme of things so whether you were offering one, two or ten if you've got a good team and the pick isn't likely to be very good then its just not that enticing.
3. You also didn't say anything about the other team who did make the trade. The scrub player was more than likely just to make the salaries work - what's important is the pick. Is it a bad team with a likely lottery pick? Again I don't know anything about at what point in your season you are (is JJJ a rookie or is this in the future) but its possible Boston knew they had to get rid of him or couldn't resign him or whatever and if a lottery pick was offered you're probably better off with a lottery pick than some ok guys and late first round picks.
4. There's a small chance the Boston GM could be a terrible GM (yes this is possible - there is the chance in the code for a GM like Isaiah Thomas to be generated) - he may have completely underestimated what you offered or overvalued what the other team offered.

There is also a chance the AI just missed something in its logic in general and needs to be tweaked. If you want to send me the save game file with the details on what you offered etc I could mess around with it and roll it back before the trade deadline just to see what the AI was thinking when it turned down your offer and took the one it did.

I guess that makes sense. I was a pretty good team, I think I ended up as the 3rd seed that year. I offered Mikal Bridges, Julius Randle, an auto-generated rookie, and 2 first round picks for I think an expiring JJJ, which was the best match for value in terms of young players/win-now players. Boston was a good team, about the same caliber as me actually. That may be why they didn't want to trade with me because I was a conference rival. But all these things that go into AI trading are really cool, even if the GM was just a bad GM that's really cool. Loving the game so far.

If you'd like me to send you the save anyway, just let me know.

I would be happy to take a look at it if you send it