[BUG] Parser skipped input between top-level statements

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

After inputing the following prompt, Claude unexpectedly displayed a permission request: "Parser skipped input between top-level statements"

test run:

cd $TMPDIR && cat > t.s <<'EOF'
.text
ldr w1, [x2]
ldr x1, [x2]
ldr x1, [x2, #16]
ldr w1, [x2, #16]
ldrsw x1, [x2, #8]
ldur x1, [x2, #-4]
ldur w1, [x2, #255]
str x1, [x2, #16]
str w1, [x2, #16]
svc #0x80
EOF
clang -target arm64-apple-darwin -c t.s -o t.o 2>&1 && otool -tv t.o 2>/dev/null | head -40

sandbox=yes
auto-allow=yes

<img width="984" height="922" alt="Image" src="https://github.com/user-attachments/assets/2128451f-1d05-4a58-ae7b-40f7f07fe6c0" />

What Should Happen?

It should automatically allow this shell command to run in sandbox.

Error Messages/Logs

"Parser skipped input between top-level statements"

Steps to Reproduce

sandbox=yes
auto-allow=yes
prompt=

test run:

cd $TMPDIR && cat > t.s <<'EOF'
.text
ldr w1, [x2]
ldr x1, [x2]
ldr x1, [x2, #16]
ldr w1, [x2, #16]
ldrsw x1, [x2, #8]
ldur x1, [x2, #-4]
ldur w1, [x2, #255]
str x1, [x2, #16]
str w1, [x2, #16]
svc #0x80
EOF
clang -target arm64-apple-darwin -c t.s -o t.o 2>&1 && otool -tv t.o 2>/dev/null | head -40

Claude Model

Opus

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.169 (Claude Code)

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_