v1.6.0: Switched the priority of Gemfile.lock and Podfile.lock for required CocoaPods version detection.
Previously if both Gemfile.lock and Podfile.lock were in the repo (in the directory of the Podfile), Gemfile.lock won and the CocoaPods version defined in Gemfile.lock was used. Now Podfile.lock wins, and Gemfile.lock is only a fallback if Podfile.lock can’t be found in the directory of the Podfile.
So new 1.6.0 version changed a bit how bitrise figuring out what version of cocoapods is needed.
Is there a way to call bundle install instead of pod install ?
Because at this momen I have scripts that have required gems. Previously this step did download them because it did calls bundle "install" "--jobs" "20" "--retry" "5", but now it is pod "_1.1.1_" "install" "--no-repo-update" "--verbose"
Is there a way to override this setting?
Do you need bundle install for CocoaPods directly?
If not, then the best is to add a Script step and simply run bundle install there, any way you want to (can be the same way as the CocoaPods step did before: bundle "install" "--jobs" "20" "--retry" "5").
You can add the Script step before or after the CocoaPods step, depending on where you need those gems.
Yup that does solved my issue 
Great to hear and thanks for the question! 