You are currently leaking multiple globals variables, here is a few:

Global variable addItemSettings tainted by Hekili - Interface\AddOns\Hekili\Classes.lua:4219
Global variable pClass tainted by Hekili - Interface\AddOns\Hekili\Classes.lua:694 NewSpecialization()
Global variable role tainted by Hekili - Interface\AddOns\Hekili\Classes.lua:694 NewSpecialization()
Global variable texture tainted by Hekili - Interface\AddOns\Hekili\Classes.lua:694 NewSpecialization()
Global variable _ tainted by Hekili - Interface\AddOns\Hekili\Classes.lua:694 NewSpecialization()
Global variable name tainted by Hekili - Interface\AddOns\Hekili\Classes.lua:694 NewSpecialization()
Global variable encodeB64 tainted by Hekili - Interface\AddOns\Hekili\Options.lua:8212
Global variable decodeB64 tainted by Hekili - Interface\AddOns\Hekili\Options.lua:8239
Global variable TableToString tainted by Hekili - Interface\AddOns\Hekili\Options.lua:8270
Global variable StringToTable tainted by Hekili - Interface\AddOns\Hekili\Options.lua:8281
Global variable Hekili_Menu tainted by Hekili - Interface\AddOns\Hekili\UI.lua:449
Global variable Display_GetPerimeterButtons tainted by Hekili - Interface\AddOns\Hekili\UI.lua:1365
Global variable Hekili_GetRecommendedAbility tainted by Hekili - Interface\AddOns\Hekili\Core.lua:1329
Global variable onInitStart tainted by Hekili - Interface\AddOns\Hekili\Core.lua:73
Global variable overcap tainted by Hekili - Interface\AddOns\Hekili\State.lua:1250 spend()
Global variable _ tainted by Hekili - Interface\AddOns\Hekili\UI.lua:940

I'd recommend running a luacheck or uploading your zip file to globe.

A few of these are intentional, but most aren't. I'll take a look. Thanks.

These should be resolved; I'll check globals again as you suggested.

Missed at least one:
Global variable name tainted by Hekili - Interface\AddOns\Hekili\Core.lua:601 GetPredictionFromAPL()

@Hekili More leaks:
Global _ set: UI.lua Line 41,43,61,1079,2267
Global f set: UI.lua Line 165
Global count set: Options.lua Line 7071,7074
Global delay set: WarlockDemonology.lua Line 308

Other issues:
and X and X: https://github.com/Hekili/hekili/blob/master/Classes/WarriorProtection.lua#L521

Table entries that are set twice/overwritten:
Line 1174 & 1177: https://github.com/Hekili/hekili/blob/master/Classes.lua#L1174
Line 1061 & 1063: https://github.com/Hekili/hekili/blob/master/Classes/HunterSurvival.lua#L1061
Line 284 & 411: https://github.com/Hekili/hekili/blob/master/Classes/HunterBeastMastery.lua#L284
Line 798 & 803: https://github.com/Hekili/hekili/blob/master/Classes/DemonHunterVengeance.lua#L798
Line 539 & 544: https://github.com/Hekili/hekili/blob/master/Classes/WarriorArms.lua#L539
Line 985 & 993: https://github.com/Hekili/hekili/blob/master/Classes/HunterBeastMastery.lua#L985

@Hekili More leaks:
PassedIndent Formatting.lua 780
DepthNext Formatting.lua 803,807
Depth Formatting.lua 805
cost_per_sec Options.lua 6838
skeleton Options.lua 7128 (and accessed on 7004)
RebuildScripts Options.lua 7922,7978,8039,8135,8139,8144

The following are global accesses:
Utils.lua 93 global k
Formatting.lua 778,798 global TabWidth
MultiLineEditor.lua 201 global MAJOR
Classes.lua 609,614 global self
Scripts.lua 93 global self
Classes.lua 4682 global i
Options.lua 7861 global index
Targets.lua 138 global range
Targets.lua 320 global spell
Options.lua 6792,6793,6882,6883 global sKey
Options.lua 7858 global key
Options.lua 8521 global accommodate_targets
UI.lua 67,1428,1477,2008 global Screen
UI.lua 189,190 global dispID
Scripts.lua 1008 global rce
Core.lua 854 global time_ceiling