It sounds to me like it's a matter of transition between mediums.
When electricity flows from a generator to a device, the device isn't receiving 100% of the electricity. Some gets lost along the way. Energy decays the longer it has to travel from one source to another, dependent on the quality of the conductor. When you store the mana in a container, it's like storing energy in a battery. Unless you had a perfect conductor that was well insulated to prevent mana from discharging en route, you can never expect a perfect 1:1 transfer.
It sounds to me like you're trying to use a poor conductor (you, a human,) to pull the mana from the corpse and transfer it into the container. Ignore the fact the mana would start leaking out of the corpse once they died; the fact that you're pulling the mana from an unsealed storage container, moving it through a conductor that lacks insulation (the mana sealing runes), and trying to direct the flow into another container (the jar with runes on it) means it's only logical that you'd lose mana in the process.
When you then try to transfer the mana into yourself, or rather your own inner container, not only are you channeling this energy through a poor conductor without insulation, but you're trying to push it into a container that you can't directly observe and are having to let the mana spray in order to possibly get it to go into the container. Here's a visual for you...
The corpse is a water source. Your hands, arms, and shoulders (creating a distinct path from hand a to hand b) that is being used to channel the mana from the corpse into the new container is the hose. The container with runes on it is Jar A. Your personal mana supply or "inner mana container" is Jar B. You yourself are a houseplant.
You know you need to fill a jar as much as possible. You can use the hose to fill up one of the two containers, but you know you'll lose some either way. The hose doesn't allow the water to exit in a nice stream, it just sprays. Fortunately, you have a clean visual on Jar A, but Jar B is hidden underneath the leaves of a nearby houseplant. You have to fill the jars from a slight distance (a couple feet or less than a meter, nothing crazy), so you can't just put the hose inside either of the jars and solve the issue like that.
By trying to fill Jar A, sure some ends up missing because the hose is faulty. It even probably had a few holes in it, so you should be glad you're not losing more than you are.
By trying to fill Jar B, most of it is being sprayed around the jar due to the things blocking it, keeping it out of sight. You have to work around the houseplant, as well as the spraying water, as well as the bad hose, AND the fact you can't clearly see the jar in the first place. It only makes sense there'd be so much more water wasted like that. It's clearly better just to go for the easy target that you can see and not have to worry about things getting in your way. Stock up on these jars of mana instead of worrying about trying to fill yourself up more. This doesn't even start into the logistics of how your internal mana container already has mana in it, so if it would exceed 100% you'd just leak it out anyways because there's no way for a jar to hold more than 100% its capacity. Just use the mana container for storage then absorb the mana when you're running low on your personal supply.
I recommend looking into the manga for Fairy Tail, as magic can be contained within one's inner "containers" (there are two, one is called a "second origin") or held in outside containers called "Lacrima." Some even have lacrimas transplanted inside themselves to have the best of both worlds. This question basically mirrors that world's mechanics, just in a darker sense.