The first issue is as designed. The problem here is that Factorio uses a different type of item for magazines, armors, repair packs, modules and a few other items. The item types used in labs are of type "tool", which has a durability and thus can be consumed by a lab. Regular items can easily be converted to a tool, but for magazines/armors/etc I had to create a duplicate item which can be consumed by labs, which uses the suffix "-siftool". Such items can't be used for their original purpose and can only be consumed in the lab. I also added a recipe to convert the original item to the "-siftool" equivalent. I did not make a specific icon yet to indicate that the duplicates are a "tool" for research.
The second issue with the missing yellow magazine has been solved in 0.1.1
Also I added a command /sif-test-deadlock which checks if all technologies can be researched given the recipes which are unlocked chronologically. With the updates in 0.1.1 the mod should be deadlock free for vanilla.