I'm just working on my polybar config, experimenting with settings just to see what happens, and I set this setting in the default polybar config:

module-margin-left = -1

I'm running Arch, with linux-lts 4.14.44, and xorg-server 1.20.0-2, with Intel hd3000 graphics using the kernel kms intel driver, without compton running (normally I would, but haven't set it up yet). I'm running a vanilla i3-gaps config (pulled via the i3 group in Arch), and am launching polybar via dmenu running polybar example, and starting my session with sddm. If there's any other info that can help, I'll share.

Just tested, this also happens on git the latest commit/version b70d5b5