If you end up with a particular expression being unevaluated, it probably means that none of the DownValues matched the expression. So, you should start looking for pattern mismatches for toRep. You defined toRep as

toRep[gen_?StringQ]

(which could have just been toRep[gen_String], by the way), so one hypothesis is that what was passed to toRep wasn't a string. Indeed, if you look at the FullForm of your result, you'll see that the arguments the toRep expressions are not strings. Here is the suspicious code:

toRep /@ ("{" <> # <> "}" & /@ s // ToExpression)

Analyze the order of operations here, and you'll find your problem.

(I'm not really sure what your strategy is here, but I'm guessing you didn't want to restrict toRep to strings.)

Thank you for pointing out this subtle difference. I tried the following method, but still failed.

In my situation, there are two wl script files opened in Mathematica. In one file, I created the following two functions and evaluated them:

toRep//ClearAll;
toRep[gen_?StringQ]:=Block[{coef,x,y,z}, 
coef=CoefficientArrays[gen,{x,y,z}]//Normal;
AffineTransform[{coef[[2]],coef[[1]]}]//TransformationMatrix
]
toReps//ClearAll;
toReps[gens_?StringQ]:=Block[{s,x,y,z}, 
s=StringSplit[gens,"\n"];
toRep/@("{"<>#<>"}"&/@s//ToExpression)
]

Then in another wl file, I evaluated the following code snippet:

In[42]:= (*
The Space Group has been identified as (No. )

Input generators
-y, -z, -x
y, -x, -z
1/8 + x, 1/8 + y, 1/8 + z

Transformation Matrix to the standard/default setting
(   
)
*)
SGGenSetWrongXYZ="-y,-z,-x
y,-x,-z
x+1/8,1/8+ y,z+1/8";

(*StringSplit[SGGenSetWrongXYZ,"\n"];
SGGenSetWrong=toRep/@("{"<>#<>"}"&/@%//ToExpression);*)
toReps[SGGenSetWrongXYZ]

Out[43]= {toRep[{-y, -z, -x}], toRep[{y, -x, -z}], 
 toRep[{1/8 + x, 1/8 + y, 1/8 + z}]}

As you can see, a portion of the result still appears as unevaluated.

Regards, Zhao