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I work for a enginering company where a few senior engineers got into a large fight that caused a lot of concern. The more senior engineer "stone walled" the not as senior engineer apparently, and the junior engineer now runs an "automation team", whose job is to find inefficencies in the company, and improve or automate them.

The junior engineer gets to pick any part of the company to improve, but he is holding a grudge against my division's most senior engineer, and keeps automating tasks for just my division. It has a lot of engineers nervous that we'll become redundant, and some of our best engineers have either transferred to other units, or quit. Our team leaders have talked to this engineer, and he insists he's not being a bully, but he's just "fixing whatever problems come to mind first". We all agree on my team that he's trying to single out our division (most of the Windows developers in the company) first in order to get our most senior engineer fired (due to not enough people under his management).

How can we approach human resources to stop this bullying behavior, or get him to automate stuff that isn't our work exclusively? My boss keeps telling the team not to worry about layoffs, but we don't believe him, and since the project is saving the company money, we don't know how to properly ask for help.

You can't stop Automation. When automation occurs in general, its aimed at increasing productivity by removing easy and repetitive tasks and allowing an employee to focus on more important work. If its the case that these automation procedures are being targeted at making people redundant, I would go back and look at any team which are under performing or struggling due to a high work load and have the automation team focus there, because there will be noticeable profits when increasing productivity, instead of trying to make people redundant.

E.g. If sales is having a hard time processing orders, automate that. It creates more work over all. If engineering is having a hard time completing all the work. Automate parts of that to increase the number of completed projects.

As your team is currently being automated then your going to have it tough. Automation usually requires there be a very well defined procedure in place, because Robots have a hard time accounting for the unknown or exceptions (there are so many exceptions). If your team is actually doing tasks that are very easily automated, I would personally look into retraining, as all industries will be looking to automate their work force (Like if your Job is literally following a manuscript, you should be slightly concerned that your aren't developing many skills or could be made redundant fairly easily).

On a more personal level (not 100% advisable), you can always make automation more difficult by not providing complete information to the team performing the automation, or suggests skips/shortcuts like skipping validation checks which can cause huge issues further down in the line, or generally refusing to work with them. I don't advise this, because its a generally shitty thing to do... but I have seen it done, specially by some more senior staff who want to ensure their job security.