2. It can mess things up if your backroom is not properly located or if there are pulls/truck waiting to be pushed.
3. Subt is best practice. EXFs have the potential to cause bad data integrity.
4a. Not pushing to the piece, not pushing to capacity, burning batches, incorrectly QMOSing, POS errors, overuse of EXFs, etc.
4b. If you meant that the system pulls too much, then your bakery sections are probably located as casestock. Changing these groupings to open stock will help with accurate pull quantities.
If you are trying to fill, scan in OUTs. Counts will not be changed. If the pogs are mpg, use stand alone PTM's to fill. If your IS team is not scanning, ask their TL what the reason is. You should not research without consulting with the Instocks TL.
I would check your capacities. Most of the bakery capacities are so screwed up right from the initial set. Expecting you to double stack and put 4 deep loafs of bread is dumb, so stores only put out maybe half that. Well the system isn't going to trigger a pull when it thinks it originally had 30 loafs of bread but only 10 were put out and now the spot is empty. Then you get to the fight the battle of well who has time to go around and record all the messed up capacities and fight with Mysupport to convince them that it needs to be changed. Plano TL, CTL, Log TL, welcome to pass the buck. Doesn't matter if you use stand alone outs, research, exfs, manual subt, if your capacities continue to be messed up you will be fighting the battle every shift.
I used stand alone research in the pfresh area while on Instocks. We got trucks M,W,F. On Tues and Thurs., I would do the pfresh area in stand alone IF everything was backstocked and pushed. This would allow me to correct drastic changes immediately so they would not wind up on the drastic count report the next day when we got another truck in and they could not be corrected. We had bakery table trouble too. It was due to the triggers being higher than the actual capacity of the table. If you never hit your trigger, nothing will ever come out. We did EXF because it was screwed up anyway.