Unfortunately that is not a lot to go on in terms of figuring out what happened, but I will make a stab at it with a bunch of guesses.
First,
Make sure all three formations were part of the same Army, i.e. Beauregard in Alexandria is a Corps Commander in the AoNV? If he is an Army stack, he will only MTSG for Corps attached to him, not friendly Armies and their associated Corps.
Second,
I attacked with all 3 armies (of course not really synchronized).
This could easily account for the result. At least two of the Corps (they better not have all been Armies or they can't MTSG each other!) need to have been marching from the same region and under "synchronized" orders so that they arrive on the same day. They can then both target enemy stacks (possibly the same one) and a large battle will commence with both Corps involved in the first round and any MTSGers coming in on the second and later rounds. If for whatever reason, they arrive on different days, they initiate battle on their own, as per your Offensive orders, but have to fight it by themselves and possibly be overwhelmed. They may or may not MTSG each other in this case, but even if they do, it is definitely better to have everyone together and able to act in the first, most important, round of the battle compared to entering in later rounds via MTSG. A stack that cannot synchronize movement to arrive on the same day should instead be optimized to MTSG: being or supporting an Army stack, being set to Offensive posture, having a commander with a high strategic rating (not sure this counts now that I think on it) and with Fast Movers and Pontoons (anything that decreases marching time increases MTSG chances).
In general, you want to stick to the principle of troop concentration, but you are constrained by CPs. In a perfect world every brigade will be in a maxed out division, and every division would be stuffed into one mega powered stack. In practice a Corps or Army stack can contain four to six divisions, not all of which are perfectly full. Since you need more than six to fight the giant battles the trick is to coordinate pairs and trios of stacks this size to enter battles with each other in the most advantageous ways. This takes a bit of practice, and is tricky by design, but once you are good at it you will crush the AI regularly, since she isn't very good at it either.
Third,
If Butler had 100,000 men then there must have been another Union Corps that MTSGd from somewhere. To find out where they came from and to better understand what else went wrong, do a little log and Battle Screen forensics.
Go to the log and locate the first battle in question. Take note of what is listed around it like "Jackson's Corps committed in Prince George, MD" and how many hits we took in retreat. Click on the sword icon to bring up the Battle Screen. Take a look at the row of enemy generals, and match them up with the divisions they command. Count how many divisions they have, and compare it to how many you have. For really big battles you need to scroll down to see them all. Note which took the most hits on both sides.
Now click the circled letter in the upper left corner and you can then see what happened on each turn. MTSG forces cannot participate until the second turn. Examine the Union forces in the battle on turn one and compare them to turn two. The new divisions (who you will note take all the hits while the forces from the first round seem to sit out the round) are MTSGers. Check out who those leaders are and see if you can remember/spot them on the map as clues to where they might have come from, and count how many divisions they have. I am guessing Annapolis from what you have said, but without a screenshot....
Also take note of which, if any, of your own forces MTSGed, and how this affected the course of the battle.
Observe that in most battles (it sounds like you have three to look at) the hits (hearts) taken by each side in the first round are noticeably higher than in later rounds. This is because during the first round elements get to fire an extra shot at each range permitted by the terrain/weather, whereas the second and later rounds only have Range 1 and Assault Phase. Take a look at the entrenchment level the opponents had and look for movement penalty icons for your guys like river crossings. Also note the number of units and elements that participated in each round.
When analyzing battle screens it is important to bear in mind that the unit of measure the game engine uses is hits (hearts). Assess casualties based on hearts, not PWR, which takes cohesion into account, or the number of "men" lost which is for flavor only and can be misleading. Count relative force size by comparing the number of divisions on each side (noting that some divisions are only half-sized) rather than totalling up the number of hearts or going by the "men."
Try to form a judgement on what went wrong overall. Did everyone MTSG like they were supposed to? Did fighting three separate battles mean you were defeated in detail? Where did everyone retreat to, where did his supporting corps come from, etc.?
I, for one, would not judge you if you took this turn back. You have invested a lot of time into this game and have gotten pretty good at it, but unfortunately the slow build up in the Grand Campaigns does not give players a lot of experience to draw on when the complex and high stakes Corps vs Corps battles start to go down. This kind of blow could be crippling, and it will take a long time to start a new game and play it to this point. On the other hand, playing it out is instructive too, and you might find that you can still find a way to win. Either way, a good postmortem will inform your play going forward.