Unfortunately, there are no provisions in the rules to avoid this situation. In my experience, the chief referee's emphasize time management and keep the match moving, but this R1 seems to be ignorant of the situation based on your description. The R1 should scan the benches for possible time-out and substitution attempts as well as the court for other issues such as a player tying a shoe or a ball entering the court.
I would discuss your experience with this R1 with the chief referee. Explain your experience with the substitution. Don't complain about the line call as there may have been several reasons that it was ruled in favor of the other team. It is possible that this R1 is inexperienced and needs some guidance on properly scanning the court and benches, and the chief referee is proper channel to provide the feedback.
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