Ok, here is the makeup of the “mslug.zip” for fba-libretro.
Does yours match this if you open up the zip?

NOTE: The roms starting with 201 need to be in the mslug.zip, and the rest will need to be in your neogeo.zip that should be in the same directory.

<game name="mslug" romof="neogeo">
		<description>Metal Slug - Super Vehicle-001</description>
		<year>1996</year>
		<manufacturer>Nazca</manufacturer>
		<rom name="201-p1.p1" size="2097152" crc="08d8daa5"/>
		<rom name="201-s1.s1" size="131072" crc="2f55958d"/>
		<rom name="201-c1.c1" size="4194304" crc="72813676"/>
		<rom name="201-c2.c2" size="4194304" crc="96f62574"/>
		<rom name="201-c3.c3" size="4194304" crc="5121456a"/>
		<rom name="201-c4.c4" size="4194304" crc="f4ad59a3"/>
		<rom name="201-m1.m1" size="131072" crc="c28b3253"/>
		<rom name="201-v1.v1" size="4194304" crc="23d22ed1"/>
		<rom name="201-v2.v2" size="4194304" crc="472cf9db"/>
		<rom name="asia-s3.rom" merge="asia-s3.rom" size="131072" crc="91b64be3"/>
		<rom name="sp-s2.sp1" merge="sp-s2.sp1" size="131072" crc="9036d879"/>
		<rom name="sp-s.sp1" merge="sp-s.sp1" size="131072" crc="c7f2fa45"/>
		<rom name="sp-u2.sp1" merge="sp-u2.sp1" size="131072" crc="e72943de"/>
		<rom name="sp-e.sp1" merge="sp-e.sp1" size="131072" crc="2723a5b5"/>
		<rom name="vs-bios.rom" merge="vs-bios.rom" size="131072" crc="f0e8f27d"/>
		<rom name="sp-j2.sp1" merge="sp-j2.sp1" size="131072" crc="acede59c"/>
		<rom name="sp1.jipan.1024" merge="sp1.jipan.1024" size="131072" crc="9fb0abe4"/>
		<rom name="sp-45.sp1" merge="sp-45.sp1" size="524288" crc="03cc9f6a"/>
		<rom name="japan-j3.bin" merge="japan-j3.bin" size="131072" crc="dff6d41f"/>
		<rom name="neo-po.bin" merge="neo-po.bin" size="131072" crc="16d0c132"/>
		<rom name="neo-epo.bin" merge="neo-epo.bin" size="131072" crc="d27a71f1"/>
		<rom name="neodebug.bin" merge="neodebug.bin" size="131072" crc="698ebb7d"/>
		<rom name="sp-1v1_3db8c.bin" merge="sp-1v1_3db8c.bin" size="131072" crc="162f0ebe"/>
		<rom name="uni-bios_3_1.rom" merge="uni-bios_3_1.rom" size="131072" crc="0c58093f"/>
		<rom name="uni-bios_3_0.rom" merge="uni-bios_3_0.rom" size="131072" crc="a97c89a9"/>
		<rom name="uni-bios_2_3.rom" merge="uni-bios_2_3.rom" size="131072" crc="27664eb5"/>
		<rom name="uni-bios_2_3o.rom" merge="uni-bios_2_3o.rom" size="131072" crc="601720ae"/>
		<rom name="uni-bios_2_2.rom" merge="uni-bios_2_2.rom" size="131072" crc="2d50996a"/>
		<rom name="uni-bios_2_1.rom" merge="uni-bios_2_1.rom" size="131072" crc="8dabf76b"/>
		<rom name="uni-bios_2_0.rom" merge="uni-bios_2_0.rom" size="131072" crc="0c12c2ad"/>
		<rom name="uni-bios_1_3.rom" merge="uni-bios_1_3.rom" size="131072" crc="b24b44a0"/>
		<rom name="uni-bios_1_2.rom" merge="uni-bios_1_2.rom" size="131072" crc="4fa698e9"/>
		<rom name="uni-bios_1_2o.rom" merge="uni-bios_1_2o.rom" size="131072" crc="e19d3ce9"/>
		<rom name="uni-bios_1_1.rom" merge="uni-bios_1_1.rom" size="131072" crc="5dda0d84"/>
		<rom name="uni-bios_1_0.rom" merge="uni-bios_1_0.rom" size="131072" crc="0ce453a0"/>
		<rom name="neopen.sp1" merge="neopen.sp1" size="131072" crc="cb915e76"/>
		<rom name="sm1.sm1" merge="sm1.sm1" size="131072" crc="94416d67"/>
		<rom name="sfix.sfix" merge="sfix.sfix" size="131072" crc="c2ea0cfd"/>

		<rom name="000-lo.lo" merge="000-lo.lo" size="131072" crc="5a86cff2"/>
	</game>