For the sake of EZ math, I'll break down the hand in the simplest form (in other words the stacks varied and leaving out "dead" money in the middle but proportionately pots/ bets are correct).

Seat A: first to act, $100 stack
Seat B: 2nd to act, $200 stack
Seat C: 3rd to act, $300 stack

HOMEGAME - NLHE Post Flop Action, 3 players:

Seat A: Check
Seat B: bet $25
Seat C: call $25

Seat A: Raise All In $100
Seat B: Raise All In $200
Seat C: Call $200

So, main pot is $300 (seats A,B,C)
side pot is $200 ($100 each seats B,C)
Money is left in front of each player. Seat A $100, Seat B $200, Seat C $200

Turn & river, Seat A has winner for main, Seat C wins side pot, Seat B is busto.

"Dealer" begins paying in the wrong order by trying to pay the main pot (3 players) first, pulling all the red out of each stack
(lets say $75 from each stack) leaving:

Seat A $25
Seat B $125
Seat C $125

"Dealer" puts reds in the middle pot. Seat C begins to scoop remaining chips in front of them. Seat B chips remain untouched after red is removed. Seat A says he is owed $25 from each remaining stack. Debate ensues, Many opinions are "disCussed". Seat A argues that after main pot is created stacks in front of Seats B & C should be equal.

Seat A decided F' it, and just send the "short pot" his way, Seat 3 has a little fit feeling that Seat A somehow got extra and throws a temper tantrum sitting out for an orbit.

Is there ever any scenario that after main pot is balanced that the 2 stacks for the side pot (Seats B & C) would not equal in size?

I say nope.

Even this simplified version leaves my liberal arts brain rather confused. Also, this is why you 1, bring in all bets and 2, separate/pay the side first. "Dealer" gets a KitN.

Is the meaning of "Money is left in front of each player. Seat A $100, Seat B $200, Seat C $200" that Seat C also still has his covering chips separate from the stack in front that represents the call of both all-ins? If so, then there are no scenarios where B &C's stacks would not be equal.

If that call isn't separated from C's stack, then B & C obv won't match.

Seat A wins the main pot for $300.00 ($100 he originally put in plus $100 from each of the other 2 players). That leaves $100 in Seat B's stack, and $200 in Seat C's stack. Since Seat B only has $100 left, that is all Seat C win's now (plus his $100.00 he contributed)

After all is said and done, the stacks should be as follows.

Seat A ($300.00)
Seat B ($0.00)
Seat C ($300.00)

edit:

Something is wrong in your example though, either this part:
"Seat A: first to act, $100 stack
Seat B: 2nd to act, $200 stack
Seat C: 3rd to act, $300 stack"

OR this part - their stacks should not be these sizes following the all ins and call, if they were originally the sizes you listed in the first part of the post:
"Money is left in front of each player. Seat A $100, Seat B $200, Seat C $200"

Yes, I can see a way. PLayer A is at the end of the table, far for the dealer to reach for. PLayer C is sitting beside the dealer. PLayer B is at the other end of the table.

Dealer grabs $200 from Player C stack and throws it towards Player A so he has his total of $300 main pot.

Player B would have $200 left and player C $100 left. Dealer pushes the remaing chips to Player C

Dang the dealer could have been gangster and just shipped B’s stack to A + main pot. C pays/wins nothing because of the side pot.

Why did the dealer take $75 from all the stacks?

If A had $100 in front of him, you could build his pot by pulling in $100 from each stack. Then for another pot, with B having $100 in front of him, you could pull in $100 from the remaining players for a side pot.