Although it would certainly help, you don't have to post the original script - but you can whittle it down to a Short, Self Contained, Correct (Compilable), Example (http://sscce.org/) that reproduces the problem. Otherwise, we'll just be guessing.

the rest of my perl script does not run

How did you determine this? Have you tried printing something just after the backticks?

instead the command starts to run again

Unless the script is programmed to go back and attempt to run the command again (the backticks are inside a loop, sub, or after a label), or the script itself is being run again through some mechanism you haven't told us about, this seems really unlikely. Have you tried running the exact same command from the command line?

I was thinking about adding something like

Better to diagnose the problem instead of attempting solutions... Basic debugging checklist

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