I had a similar problem with this last season.
U15 red v white. At a period in the game both managers seemed to be making a sub ever other stoppage, it was getting a bit tedious, then ball goes out for a white throw in, reds make a sub, I stop concentrating and I wait for the red player to leave the pitch and the sub enters the pitch and I restart.
Next thing I know a long throw comes in to the opposite side of the field where a striker is unmarked and heads it home to make the score 2-2. Cue screaming from the managers and players that their left back wasn't t in position from the sub. Was I wrong in law, technically no the sub was complete, did I do the wrong thing? Yes, so I apologised profusely and everyone seemed to accept it from then on. Luckily reds made it 3-2 so I didn't cost them the game
The thing I learned from the situation, in junior football or with any rolling subs game, ask the manager to give you a thumbs up when he's happy, especially when they make multiple subs from both teams.
Take your time and only restart when you are ready and happy everyone is set and in position.