I assume if a character suffers knock back and is moved from the square containing the Web Special Terrain Marker then the Web Special Terrain Marker is removed, but if a character suffers knock back but does not move from the square containing the Web Special Terrain Marker (because there is a character/wall/blocking terrain in the first square of the knock back path) then the Web Special Terrain Marker stays?

Web Special Terrain Marker: A character occupying this square must break away for movement purposes. Immediately after the character occupying this square no longer occupies it, remove this marker from the map.

If the square is still occupied, the token is not removed.

Here is why it matters if the Web Special Terrain Marker is put in one square or two....

. . . . .
. . . . .
. . . B .
. . . D .
. . . . .
. . S I .

(S)pider-Man successfully hits (D)ouble-base character in square D with First Webs. A Web Special Terrain Marker is placed in square D. (The question is...is a Web Special Terrain Marker placed in square B as well?) (I)ceman then hits (D)ouble-base character in square D for 1 damage with a ranged combat attack. (D)ouble-base character has Combat Reflexes and wants to take knock back. Following the knock back, it looks like this.

. . . . .
. . . B .
. . . D .
. . . X .
. . . . .
. . S I .

The Web Special Terrain Marker that had been placed in square D is now removed (the square is marked by the green X above.) If a Web Special Terrain Marker had been placed in both squares occupied by the double-base character, then the double-base character is still on a Web Special Terrain Marker (in the red square) and would need to roll a break away next turn if it wanted to move. If only one Web Special Terrain Marker was placed, then the double-base character is no longer on a Web Special Terrain Marker and would not need to roll break away if it wanted to move next turn.

So, if a multi-base character is hit by First Webs, do you put a marker in each square occupied by the multi-base character or just the square hit?

In that respect, the entire character is "webbed" and as soon as it moves from its current location, it would lose the web terrain marker. Therefore, from that perspective, the web terrain marker is in both squares and as soon as he moves out of either one, all of the terrain markers are gone.