It sounds like you are describing the needle holes left behind from removing some quilting stitches the LAer wasn't happy with. Hard to tell without a photo. But a light spritz with a misting bottle is usually all it takes to get those holes to close up. If the misting doesn't work, they usually close up with washing as Peckesh said. I have also gotten them to close up by running my fingernail over them.
The needles used by a LA machine are much larger than regular sewing machine needles. So they tend to move those warp and weft threads a lot more than your DSM needle. It is especially evident on tight weaves like batiks.