How does InDesign Grep represent groups greater than 9?

In InDesign GREP replacements, the captured found text only works from $1 to $9.

So $12 is not treated as “capture group 12”. In many cases it is read as $1 plus the literal number 2, or ${12} is treated as plain text.

So yes, this is basically a limitation.

The workaround is to only capture the parts you actually need, and make the rest non-capturing groups.

For example, instead of this:

(A) (B) (C) (D) (E) (F) (G) (H) (I) (J) (K) (L) (M) (N)

Use this:

(A) (?:B) (?:C) (?:D) (?:E) (?:F) (?:G) (?:H) (?:I) (?:J) (?:K) (L) (?:M) (?:N)

Then replace with:

$1$2

This gives:

AL

The important part is that only A and L are captured, so they become $1 and $2.