Not sure if it is a bug, incompatibility, or just my combo of mods. But when using auto module inserter mods I've noticed a few things. When using them on a building on the green "any" tile they work fine but if anywhere else they only remove modules that don't match. (Other tile types and open world miners/pumpjacks.) However my mining-patch-planner mod still inserts modules fine. I've included a list of the mods in my save along with their versions. I've tried an alternative for some of the related mods with no obvious change in behavior.
base 1.1.107
aai-containers 0.2.11
aai-loaders 0.1.4
alien-biomes 0.6.8
atan-wood 0.3.1
big-mining-drill 0.1.1
Blueprint-Editor 3.1.0
bobinserters 1.2.0
even-distribution 1.0.10
factorio-crash-site 1.0.2
FactorySearch 1.11.0
FasterStart 1.1.3
flib 0.14.1
informatron 0.3.4
k2-wind-turbine 0.0.1
mining-patch-planner 1.6.7
RampantArsenal 1.1.6
redo 0.2.13
RPGsystem 1.3.5
space-exploration-graphics 0.6.18
speed-settings 1.1.2
Squeak Through 1.8.2
Teleporters 1.0.5
WellPlanner 1.1.6
ammo-loader 1.1.42
ArmouredBiters 1.1.9
Explosive_biters 2.0.5
k2-wind-turbine-speed 0.0.3
ModuleInserterEx 6.1.2
rampart_heavy_wall 0.1.0
RateCalculator 3.2.5
RecipeBook 3.5.8
Warp-Drive-Machine 0.2.7