question

It would be quite nice if FlexSim were able to detect this situation and actually hold the items earlier so that they don't intersect. Until then, two possible workarounds are:

1. Put the transfer on the side of the conveyor

On the upside, you can put this conveyor in exactly the same position as it was, the only difference being that instead of aligning the end with the main conveyor (sweep angle of 90 degrees) you stop it a little early so that the transfer is at the edge of the conveyor. This will hold the red items correctly; the downside of this is that the items will go through a slightly odd motion when they actually enter - an interesting combination of rotation and translation. Possibly you can get this right by playing with the properties of the transfer to make it a side transfer again rather than the inline transfer it automatically becomes (setting the max angle to 40 already helped for me).

2. Use Areas

The other option is to keep the layout as you had it before, except you use an area to manually block the items. The best option there is probably Acquire / Release area, where the Area Claimer is the conveyor rather than the item. The downside is that you don't get FIFO merging anymore - once one item has entered the area all items following it may pass as well which can lead to the other side having to wait. You can mitigate this by playing with the area settings a little bit, I already made a slight improvement of giving the main conveyor priority in acquiring the area, but it still doesn't look as smooth as the default transfer point does. You could probably finetune this even more by using the Process Flow template for slug building, which does things like looking ahead to minimize the gap times, but that gets quite complicated quite quickly.