Why llvm emits the fixup referring to nop or nop-like instruction?

Compiled Xalan (one of SPEC2006 programs) with llvm 3.9.0,
I have discovered the fixup of the jmp instruction at 0x4143FF is pointing to nop instruction (at 0x414175)
instead of the next instruction at 0x414180.

.text:0000000000414175 66 66 2E 0F 1F 84 00 00 00 00 00 nop word ptr [rax+rax+00000000h]
.text:0000000000414180 49 8B 06 mov rax, [r14]

.text:0000000000414183 48 8B 98 F8 00 00 00 mov rbx, [rax+0F8h]

.text:00000000004143F7 48 89 DF mov rdi, rbx
.text:00000000004143FA E8 91 E2 FE FF call ___cxa_throw
.text:00000000004143FF E9 71 FD FF FF jmp loc_414175

The following is another example that the unconditional branch (0x460025) points to nop-like instruction
(xchg ax, ax @0x46003e) instead of the next instruction (0x460040).

.text:0000000000460025 EB 17 jmp short loc_46003E

.text:0000000000460027 31 ED xor ebp, ebp

.text:0000000000460029 E9 CB 02 00 00 jmp loc_4602F9
.text:000000000046002E 66 90 align 10h

.text:0000000000460030 8D 50 01 lea edx, [rax+1]

.text:0000000000460033 41 89 54 24 04 mov [r12+4], edx
.text:0000000000460038 89 C0 mov eax, eax
.text:000000000046003A 66 89 2C 41 mov [rcx+rax*2], bp

.text:000000000046003E 66 90 xchg ax, ax
.text:0000000000460040 48 8B 7B 50 mov rdi, [rbx+50h] ; this

Xalan is the only case that has this particular issue of all SPEC - 13 fixups in total point to 3 locations that contain
either nop or nop-like instructions. I understand there is no problem to execute the binary but
why LLVM emits the binary that has fixups referring to NOP (I think it’s a MC alignment fragment),
not a legitimate code fragment (or logical basic block)? Is this expected?