You need a subjunctive here, so it should be 'wouldn't be' not 'couldn't be'.

"Because he was afraid that his friend couldn't be on time to board the plane, he called to make a fake bomb scare." I would separate the sentence into a conditional (separated by the comma ",") just so it flows better.

He was afraid of that his friend couldn't be on time to board the plane so he called to make a fake bomb denouncement.

Thank you Nathalie

It's very good, I would just write it as follows: "He was afraid his friend wouldn't board the plane on time so he called to make a fake bomb scare."