Itinerary mistake in Netherlands / Belgium

Personally, I don't see where you think you made a mistake. I see no advantage to returning to Amsterdam for the return trip or am I missing something. You original schedule is pretty much what we would have done. We almost always fly open-jaw. Why spend money and especially time returning to the starting point or making a long run to the end of the line and then working your way back. The only difference is that we would stay in Haarlem instead of Amsterdam. We just like the ambiance of Haarlem in the evening after a busy day in Amsterdam. Being there three time and will be back this fall.

Open jaw, flying in one place and out of another, is often more efficient in time and/or ground travel distance than doing a round trip. Sounds like still a good trip in the works. So do you have an option on that Sunday of stopping in Bruges/Brugge and/or Gent, on the way to Brussels for the night? You’ll still have a full Monday, day and night, in Brussels itself. Enjoy your trip and all you’ll be seeing and doing, even the way you have things reserved!

If you plan to visit a museum in Brussels, you'll have the Sunday for that. The Monday can be used for a day trip to Brugge, which is only 1 hr away.

I think your itinerary is great. I would definitely get to Haarlem (check out Ten Boom House in Rick's book - wonderful). Also, if you have the time, I would definitely get to Bruges, without a doubt.

I'm not sure what you're second-guessing. It sounds like you are flying into A'dam and out of Brussels and that you think maybe you have a day too many in A'dam and in Brussels and one too few in Antwerp. That's not a big deal. First of all, there's plenty to see and do in A'dam and you can day trip to Utrecht or Rotterdam if you really don't want to spend time in A'dam. If you don't want to spend the day in Brussels, it's easy enough to day trip to Ghent from there (1/2 hour on the train while from Antwerp it's an hour).

There are dozens of tweaks and nuances to any traval itinerary. Yours looks fine. Accept it.
Train travel day trips save you from unpacking more often, but at the cost of time and money to keep returning to point A. If you are second guessing now, is it because there is some super deal on a Amsterdam return flight that you now see and 'think' you missed out on?
Netherlands is so small, that if you find you have seen all that is interesting to you, then add a train day trip somewhere else. Don't anticipate problems now where there most likely aren't any. Alternatively, focus on lesser known sites or museums or do some activity like biking into the country for a day. Think salvage, not reinvent.