I assume you are using Continuous WebJobs and not Manual/Scheduled. In that case, it will run on all the instances at once. For this to happen correctly, you need to be running in Standard mode, and have the Always On setting enabled.
If you don't want it to run on all instances, you can set it to be in 'singleton' mode by creating a file called settings.job
alongside your WebJob files. It should contain:
{ "is_singleton": true }
Note that when using the Kudu Process Explorer UI, you are connecting to a single instance, and won't see processes from other instances. Instead, use the Processes UI built in the Preview Portal (https://portal.azure.com/), which shows processes in all instances.