Ok I have this setup:

❯ tree -a -I node_modules
.
├── A
│   ├── .eslintrc
│   └── a.js
├── B
│   ├── .eslintrc
│   └── b.js
└── package.json

A/.eslintrc:

---
rules:
  no-unused-vars: [2, {vars: local}]  # Allow defining globals

A/a.js:

var a = 1;

B/.eslintrc:

---
parser: babel-eslint

B/b.js:

var b = 2;

package.json:

{
  "dependencies": {
    "babel-eslint": "^3.1.19",
    "eslint": "^0.24.0",
    "esprima": "^2.4.0",
    "esprima-fb": "^15001.1.0-dev-harmony-fb"
  }
}

Running eslint on dir A and B gives the expected result:

❯ $(npm bin)/eslint A B

B/b.js
  1:4  error  b is defined but never used  no-unused-vars

✖ 1 problem (1 error, 0 warnings)

however, running it on dir B and A gives an additional unexpected error on a.js:

❯ $(npm bin)/eslint B A

B/b.js
  1:4  error  b is defined but never used  no-unused-vars

A/a.js
  1:4  error  a is defined but never used  no-unused-vars

✖ 2 problems (2 errors, 0 warnings)

This only happens when using babel-eslint as the parser for directory B. I've tried the default parser, esprima, and esprima-fb and it does not throw the error for a.js. The result shouldn't change given the order of directories given to eslint right?