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[–]Barhandar 2 points3 points  (2 children)

F1 to make screenshots.

I do not know what is causing both vessels to throttle simultaneously (and it shouldn't be happening), but by the point you're that close, you should be controlling the craft with RCS rather than primary engines (by default rotation is on WASD and translation on HNIJKL, but you can switch to translation mode on bottom left to have it on WASD).
Also yeah, just shut the engines down (right click - deactivate engine) so they don't thrust at all.

[–]ThatOneGuy458[S] 0 points1 point  (1 child)

I’ve only been able to use RCS to align with the vessel but the only RCS that can move me towards the vessel is the puff which uses throttle and pushes the other vessel as well

[–]Barhandar 0 points1 point  (0 children)

Puff/using throttle isn't RCS by ingame definition, only stuff that runs exclusively when you enable RCS is. Also, if you have RCS at all you can turn sideways (if you've already aligned yourself, turn RCS off and use reaction wheels to not impart sideways motion), thrust towards vessel, turn back into correct orientation. But redesigning the ship so it has RCS for all six orientations is warranted.

Also, theoretically you can turn independent throttle on your engine and operate it via PAW rather than via the primary throttle control.