I recently put a leader on my BC so I can retie a little more without worrying about wasting braid. Well the leader knot sometimes gets snagged in a cast and it turns into a huge backlash. How do i prevent this because I actually like the leader. Any help is appreciated. Thanks!

What knot are using to join your leader and main line?

Use an Alberto and cinch slow and in control. Shouldn't be bulky in size. Or just fish straight braid and remove the issue. You can always use a snap on that setup if it permits

If the leader know is getting hung, maybe the "micro" guided rod isn't the proper tool for your application.  The guides are possibly too small to freely pass the connection.  Don't know what rod you're using but the MicroMagic rods are ridiculous both in number and size of guides.  I join 10/2 powerpro to 6# leader with a uni-uni on my spinning rods and they pass fine through 3.5mm SiC and 4mm Alconite guides with just a slight tic.

I'm using the yucatan knot. And the rod is a falcon buccoo.

Also, I can't use speed clips all the time due to changing from cranks to spinnerbaits. So I sometimes have to cut the clip of. I'm only doing this till I buy another BC.

I tied the Yucatan knot and the Alberto knot both using 50lb 832 and 20lb CX as a test to see if there was a visual diameter difference. It appears to me that the Alberto is just slightly smaller in diameter, but I don't know if it would be enough to be noticeable during casting through micro guides.    Might be worth your time to try out the Alberto.

With the micros, I would either use less of a leader so it doesn't have to travel thru the guides, or just go straight braid.

I use straight braid on my micro guide rods (frogs, etc.), and only use a leader on the macros.  The micros are just too narrow to permit passage of any type of leader knot (and I've tried them all).  You can also go to straight mono/flouro on your micros. 

As soon as i get a new setup, the leader is gone. lol It's a pain to deal with a backlash from the knot getting snagged going through a guide. But i  may shorten the leader a bit so there is less to get snagged up.

A leader on a micro, unfortunately don't mix. Like Deak mentioned, use a short leader, or go straight of the line of your choice.