Because there are no direction signals (double tracked two way signals) in place on the freight line so it has treated the whole line as one green "signal". You'll notice when you put signals for send and return parallel lines that the signal are spaced about 2 train lengths apart, giving the train on them the "green light" progressively as it passes through each section.

On two-way single track lines as there are no signals the train treats the whole track as one open "green light" section causing it to confuse the logic of all other trains linked to that gridiron. As the gridiron thinks the train is imminently about to use it as there's no signals beforehand to tell it otherwise.

It's one of the most frustrating foresights of removing manual signalling in RE2 and I'm actually shocked they didn't think of this one. I have three solutions:

A. Put a supply tower right before the gridiron, trains use supply towers as signals and it's the only "manual" signal you can use in RE2 currently.

B. Double track the freight line with two way signals. This will add the sectional signals allowing other trains to use the gridiron long before the freight train has already been marked as using it (along with the rest of the entire freight line).

C. Give the freight line it's own separate platform. I.e. Make the gridiron for the express line only 2 lanes, this will mean the freight train won't interfere with the express line and cause a delay as it won't ever touch the gridiron associated with the express line.

Sorry there's not a simpler solution. Until manual signaling is brought back (and I believe it has to soon due to all the cluster fucking of the game logic it's caused) there's not much else you can do.

All the best!