The bugged mobs thing is very very weird, I hain't seen that.
The best thing to do with a mine is to ensure EVERY square inch is lit. Us doors to block off areas that connect to natural caverns, abandoned mines.
Next time you get in, yell... I would be more than happy to help. You want to do a branch mine, and use doors to segregate it off.
What I would do is make a room at the bottom of your ladder (assuming your mineshaft is a ladder). Make like like an 8 to 16 by 8 to 16 room that is well lit and enclosed (use wooden doors). I also pressure plate the inside of the door (2 planks side by side in a crafter or your inventory crafter). (If your goat rodeo is all around this area, just make a small room here, to ensure you don't get butthumped as soon as you jump off the ladder at the bottom) If your mineshaft base is NOT like in the middle of a wide open area - this is kind of hard to explain... basically, when you get to the bottom, are there already paths in each direction?
If the whole area is a mess, you'll need to make a mining base away from there. If, say, you haven't dug in one direction (Say your mess is all east), and you can dig a fresh area in another direction, then you can use that area as your mining base.
It may be best to just abandon that mineshaft altogether and make another one (Like on that first hill we came to before you moved into the mountain, etc).
For the pressure plates, you put the plate in front of the door on the inside (secure side). Then, when you walk out, it will auto open/close. When you come back to the room, you simply right click the door. As you walk through, the plate will auto-close it behind you. This means that you (or some other butt monkey) won't accidentally leave the door open)
So, just focus on making your mining base for now. If you are in doubt, just start over and leave that place as a poignant message of the dangers of going bat shit insane underground. You should have seen some of my enormous messes on the last server =/
So, wherever your actual mining base ends up being, build out a nice 16x16ish room, make the ceiling 4 to 6 high. Bring a whole stack of logs, torches, and enough iron or cobble to make tools as needed. You should get plenty of cobble from clearing out the area (unless you end up in a cavern). Bring an iron block, or if you are low on iron, just make one as soon as you can. Bring two buckets of water, and a good amount of food. If you are hardcore tunnelrat style, bring a stack of dirt and at least a dozen seeds (you can do it with just a few, but it takes longer to get it up to max production) to make an underground farm. (If you do a farm, you'll need to make a room off to one side about 7 wide by 16 or so deep, make the ceiling at least 5 high). Bring like 8 saplings and ~32 bonemeal and make another room the same size as above, but make it 16+ deep, and make the ceiling like 10-12 high. You'll need to torch the hell out of both of these rooms (glowstone is even better)
My standard build out for a mine I plan on using a lot versus a small remote mine is:
8 double chests - Make signs for these labeling what is in each.
You want to make ~8-16 furnaces if you are going to be making stone or stone brick. If not, 2-4 is fine.
Build a water pool 2x2x1:
[XO]
[OX]
I usually just make this in the floor, place the water where the X's are, and it will fill in the O's, and you'll have unlimited water.
Now, pick a side of the room to be your main crafting area. (I usually do the opposite side as the first branch mine tunnel). Put two chests there with a crafting bench and repairinator between them. Label one chest something to the effect of gems/metals blah blah... expensive shit, "Finished Goods" -> Put things like diamonds and smelted ore in here (I put redstone/obsidian/lapis in there too) Once you get a shit ton of redstone/obsidian/etc make a separate chest or move them to your house.
The other chest is your working chest. Put coal in there, as well as extra tools, cobble you are going to cook, finished stone/stone bricks -> Make a stone/stone brick chest later, or move it to your house/sell it.
Now, throw furnaces either into the wall or on either side.
On the opposite side of the room, start your storage shit (I usually start this on the initial branch tunnel side, and then expand as shit fills up)
Make 2 double chests labeled cobble, one or two for dirt, one for gravel, and one for trash/misc (treasure hunter stuff from digging, etc)
Then start your branch mine.
Here is the basic layout:
