If you watch the footage, the stone with the lines facing forward shown up close is placed in the center (nose). Indy initially steals the stone from the left eye socket before he's captured and my screen capture clearly shows white lines on it as he turns it while putting it in his bag. The right eye socket stone has all three lines clearly visible in the footage (photoshop arrows pointing to them) and you can see them on the one Indy is removing too if you look closely.
So, either they switched the stones after the fact or at least two of them have lines on them. It's also possible there are indentations for lines that weren't painted that show up when lit, but that doesn't explain the bag shot of the left eye stone that clearly has a white line drawn in that groove versus the dude holding a white line version out to see and clearly placing it it in the nose position, which ironically has the least evidence of lines on it in the closeups
As for the argument the villagers drew the lines, just because the village one has lines doesn't mean the villagers drew them. That might even be sacrilege. The legend already existed which means even if lost, they weren't always in that mine, but likely just hidden there. Sankara received all five of them from Lord Shiva, originally with magic properties to fight evil.
Real Shiva Lingas in India (you can buy them on eBay easily enough) are stones usually formed by turning water in rivers, although some are from meteorites.
