If a resource is created by processResources, and then moved to be created by a task that is a dependency of processResources, the file will first be created by the new task and then incorrectly removed by processResources on the next build. The following build everything will work again though.
Regardless of whether this is classed as a bug or not, you should never have two tasks writing to the same place. It breaks incremental build. This is better…
task(copyInput, type: Copy) {
from 'input.txt'
into "$buildDir/input"
}
processResources {
from copyInput
from 'anotherInput.txt'
}