My summon command says (about 50% of the time) unable to summon object minecraft 1.12.2

so... I rewrote your first command so that it is more readable:

/summon Skeleton ~ ~3 ~ 
{
    CustomName:"Enemy",
    CustomNameVisible:1,
    ArmorItems:
    [
        {},
        {},
        {},
        {
            id:"minecraft:leather_helmet",
            Count:1b,
            tag:
            {
                Unbreakable:1,
                display:
                {
                    color:0
                }
            }
        }
    ],
    HandItems:
    [
        {
            id:"minecraft:bow",
            Count:1b,
            tag:
            {
                Unbreakable:1,
                ench:
                [
                    {id:48,lvl:2999}
                ]
            }
        },
        {
            id:"minecraft:totem_of_undying",
            Count:1b,
            tag:
            {
                display:
                {
                    Name:"Life",
                    Lore:["For Another Life"]
                }
            }
        }
    ],
    ArmorDropChances:[0.085F,0.085F,0.085F,0.0F],
    HandDropChances:[0.0F,2.0F],
    UUIDLeast:0L,UUIDMost:0L,
    ActiveEffects:
    [
        {Id:11,Amplifier:2999,Duration:100,ShowParticles:0b}
    ]
}

All your brackets are balanced, so that's all fine. I do notice that some of the values don't have a type identifier behind them, which isn't Always necessary, but I usually just do it. It's good practice.

You give this skeleton both a UUIDLeast of 0 and a UUIDMost of 0 Notice that UUID stands for Unique User ID. This means that every entity needs a unique UUID. You are summoning skeletons with the same UUID, which is not possible.

But further than that, your command looks completely fine.

Have you been using a command block? If you are using this command in regular chat, it may not work depending on the command since I believe there is a character limit. If this is the case, you can get a command block with /give @p command_block

Hope this helps :)