The docs read:

"any parent configuration files are ignored"

with a few exceptions, all of which do not apply in the following example (both files have a [tool.ruff] section, --config is not used, a config file is found in the filesystem hierarchy, and nothing is provided on the command line at all).

Still,

mkdir -p bug1/bug2
echo '[tool.ruff]' > bug1/pyproject.toml
echo 'select = ["ALL"]' >> bug1/pyproject.toml
echo '[tool.ruff]' > bug1/bug2/pyproject.toml
echo 'ignore = ["D203", "D212"]' >> bug1/bug2/pyproject.toml
cd bug1/bug2
ruff .

gives

warning: `one-blank-line-before-class` (D203) and `no-blank-line-before-class` (D211) are incompatible. Ignoring `one-blank-line-before-class`.
warning: `multi-line-summary-first-line` (D212) and `multi-line-summary-second-line` (D213) are incompatible. Ignoring `multi-line-summary-second-line`.

although one of each pair of rules is clearly disabled in bug1/bug2/pyproject.toml.

rm ../pyproject.toml 
ruff .

works fine, suggesting that the presence of the parent config does play a role although it should not.

ruff 0.1.5