I just found a really annoying hotkey bug while playing as Protoss. I tried Zerg too and didn’t encounter any problems.
I play with a costumized grid, so that the buildings and unit production completely follows the grid scheme. As soon as I bind my warpgates to “3”, and the warpgate upgrade is done ofc, I can’t built anything with the “w” button anymore. When I try to build an assimilator f. i., the next thing that happens is, that I have all my warp gates selected. The same happens with every other thing I tried to build with the “w” button (upgrades, units, I did not try abilities though).
Edit: I carefully rebuilt my Hotkey setup from scratch now and I still have the same problem 
If helpful, here is my hotkey setup:
Hotkey Setup
[Settings]
[Hotkeys]
ArmySelect=
ControlGroupAppendAndSteal0=Alt+0
ControlGroupAppendAndSteal1=Alt+1
ControlGroupAppendAndSteal2=Alt+2
ControlGroupAppendAndSteal3=Alt+3
ControlGroupAppendAndSteal4=Alt+4
ControlGroupAppendAndSteal5=Alt+5
ControlGroupAppendAndSteal6=Alt+6
ControlGroupAppendAndSteal7=Alt+7
ControlGroupAppendAndSteal8=Alt+8
ControlGroupAppendAndSteal9=Alt+9
ControlGroupAssignAndSteal0=Control+Alt+0
ControlGroupAssignAndSteal1=Control+Alt+1
ControlGroupAssignAndSteal2=Control+Alt+2
ControlGroupAssignAndSteal3=Control+Alt+3
ControlGroupAssignAndSteal4=Control+Alt+4
ControlGroupAssignAndSteal5=Control+Alt+5
ControlGroupAssignAndSteal6=Control+Alt+6
ControlGroupAssignAndSteal7=Control+Alt+7
ControlGroupAssignAndSteal8=Control+Alt+8
ControlGroupAssignAndSteal9=Control+Alt+9
IdleWorker=P
StatusOwner=
TownCamera=BackSlash
CameraSave0=Shift+F1
CameraSave1=Shift+F2
CameraSave2=Shift+F3
CameraSave3=Shift+F4
CameraView0=F1
CameraView1=F2
CameraView2=F3
CameraView3=F4
[Commands]
AWrp=Y
AdeptHallucination/Sentry=E
AdeptPhaseShift/Adept=E
AdeptResearchPiercingUpgrade/TwilightCouncil=E
AmorphousArmorcloud/Infestor=Q
AnionPulseCrystals/FleetBeacon=Q
ArchonHallucination/Sentry=S
Assimilator/Probe=W
AutoTurret/Raven=
Baneling/Zergling=Y
BanelingNest/Drone=F
BatteryOvercharge/Nexus=C
BlindingCloud/Viper=E
Blink/Stalker=E
BroodLord/Corruptor=Y
BuildCreepTumor/Queen=Q
BuildCreepTumorPropagate/CreepTumorBurrowed=Q
BunkerLoad=F
BurrowDown=F
BurrowLurkerMP=F
Carrier/Stargate=T
CausticSpray/Corruptor=E
ChannelSnipe/Ghost=
Charge/Zealot=Y
ChronoBoostEnergyCost/Nexus=Y
Colossus/RoboticsFacility=R
Contaminate/Overseer=D
Corruptor/Larva=D
DarkShrine/Probe=Y
DarkTemplar=S
DarkTemplarBlink/DarkTemplar=E
DisableBuildingAttack/Baneling=C
DisruptorHallucination/Sentry=V
Drone/Larva=Q
EnableBuildingAttack/Baneling=X
EvolutionChamber/Drone=S
EvolveAmorphousArmorcloud/InfestationPit=E
EvolveAnabolicSynthesis2/UltraliskCavern=W
EvolveCentrificalHooks/BanelingNest=Q
EvolveChitinousPlating/UltraliskCavern=Q
EvolveDiggingClaws/LurkerDenMP=Q
EvolveGlialRegeneration/RoachWarren=Q
EvolveGroovedSpines/HydraliskDen=Q
EvolveInfestorEnergyUpgrade/InfestationPit=Q
EvolveMuscularAugments/HydraliskDen=W
EvolveTunnelingClaws/RoachWarren=W
Explode/Baneling=Y
Extractor/Drone=W
FaceEmbrace/Viper=W
Feedback/HighTemplar=W
FleetBeacon/Probe=S
ForceField/Sentry=E
Forge/Probe=S
FungalGrowth/Infestor=E
Gateway/Probe=A
GatherProt=U
GenerateCreep/Overlord=X
GenerateCreep/OverlordTransport=X
GravitonBeam/Phoenix=E
GreaterSpire/Spire=Y
GuardianShield/Sentry=W
Hallucination/Sentry=Q
Halt=
Hatchery/Drone=Q
HighTemplar=A
HighTemplarHallucination/Sentry=A
Hive/Lair=Y
Hydralisk/Larva=A
HydraliskDen/Drone=Q
Hyperjump/Battlecruiser=
Immortal/RoboticsFacility=E
ImmortalHallucination/Sentry=T
InfestationPit/Drone=W
Interceptor/Carrier=Y
Lair/Hatchery=Y
Larva=Q
LoadOutSpray=Z
LocustMPFlyingSwoop/LocustMPFlying=E
LurkerCancelHoldFire/LurkerMP=C
LurkerHoldFire/LurkerMP=X
LurkerMP/Hydralisk=Y
MassRecall/Mothership=Y
MorphBackToGateway/WarpGate=X
MorphMorphalisk/Queen=W
MorphToOverseer/Overlord=Y
MorphToOverseer/OverlordTransport=Y
MorphtoObserver/Observer=E
MorphtoObserverSiege/Observer=W
MorphtoOverlordTransport/Overlord=C
MorphtoOverseerNormal/Overseer=W
MorphtoOverseerSiege/Overseer=Q
Mothership/Nexus=W
MoveHoldPosition=G
MovePatrol=T
Mutalisk/Larva=S
MutateintoLurkerDen/Drone=E
NeuralParasite/Infestor=W
Nexus/Probe=Q
NexusMassRecall/Nexus=X
NydusNetwork/Drone=S
Observer/RoboticsFacility=Q
Oracle/Stargate=W
OracleBuildStasisTrap/Oracle=W
OracleHallucination/Sentry=X
OracleRevelation/Oracle=Q
OracleWeaponOn/Oracle=E
Overlord/Larva=W
ParasiticBomb/Viper=D
Phoenix/Stargate=Q
PhoenixHallucination/Sentry=F
PhotonCannon/Probe=X
Probe/Nexus=Q
ProbeHallucination/Sentry=Q
ProtossAirArmorLevel1/CyberneticsCore=W
ProtossAirWeaponsLevel1/CyberneticsCore=Q
ProtossBuild/Probe=Y
ProtossBuildAdvanced/Probe=X
ProtossGroundArmorLevel1/Forge=W
ProtossGroundWeaponsLevel1/Forge=Q
ProtossShieldsLevel1/Forge=E
PsiStorm/HighTemplar=E
PurificationNovaTargeted/Disruptor=E
Queen=W
Rally=H
Ravager/Roach=Y
RavagerCorrosiveBile/Ravager=E
RavenShredderMissile/Raven=
Repair=
ResearchBurrow=T
ResearchCharge/TwilightCouncil=Q
ResearchDarkTemplarBlink/DarkShrine=Q
ResearchGraviticBooster/RoboticsBay=Q
ResearchGraviticDrive/RoboticsBay=W
ResearchLurkerRange/LurkerDenMP=W
ResearchNeuralParasite/InfestationPit=W
ResearchPsiStorm/TemplarArchive=Q
ResearchStalkerTeleport/TwilightCouncil=W
ResearchVoidRaySpeedUpgrade/FleetBeacon=W
ResearchWarpGate/CyberneticsCore=Y
ReturnCargo=I
RoachWarren/Drone=D
RoboticsBay/Probe=D
RoboticsFacility/Probe=E
Sentry=W
ShieldBattery/Probe=C
ShieldBatteryRecharge/ShieldBattery=Q
SpawnChangeling/Overseer=E
SpawningPool/Drone=A
SpineCrawler/Drone=Y
SpineCrawlerRoot/SpineCrawlerUprooted=F
Spire/Drone=A
SporeCrawler/Drone=X
SporeCrawlerRoot/SporeCrawlerUprooted=F
Spray=Z
Stalker=E
StalkerHallucination/Sentry=R
Stargate/Probe=W
Stim=
StopGenerateCreep=X
StopPlanetaryFortress/PlanetaryFortress=
SummonNydusWorm/NydusNetwork=E
SwarmHostBurrowDown=F
SwarmHostMP/Larva=G
Tempest/Stargate=R
TempestResearchGroundAttackUpgrade/FleetBeacon=E
TemplarArchive/Probe=A
TemporalField/Mothership=E
Transfusion/Queen=E
TransportMode/WarpPrism=Q
TwilightCouncil/Probe=Q
Ultralisk/Larva=X
UltraliskCavern/Drone=Y
UpgradeToPlanetaryFortress/CommandCenter=
UpgradeToWarpGate/Gateway=Y
Viper/Larva=Y
ViperConsume/Viper=Q
VoidRay/Stargate=E
VoidRayHallucination/Sentry=D
VoidRaySwarmDamageBoost/VoidRay=W
VoidSwarmHostSpawnLocust/SwarmHostMP=E
WarpInAdept/Gateway=R
WarpInAdept/WarpGate=R
WarpPrism/RoboticsFacility=W
WarpPrismHallucination/Sentry=Y
WarpinDisruptor/RoboticsFacility=T
WeaponsFree/Ghost=
Zealot=Q
ZealotHallucination/Sentry=W
ZergBuild/Drone=Y
ZergBuildAdvanced/Drone=X
Zergling/Larva=E
overlordspeed=A
zergflyerarmor1=W
zergflyerattack1=Q
zerggroundarmor1/EvolutionChamber=E
zerglingattackspeed/SpawningPool=W
zerglingmovementspeed/SpawningPool=Q
zergmeleeweapons1/EvolutionChamber=Q
zergmissileweapons1/EvolutionChamber=W