This lines:

public Collection<PSObject> InvokeScript(string script, params object[] args)
{
    return InvokeScript(script, true, PipelineResultTypes.None, args);
}

Pass args parameter into input parameter of called function, thus mixing them up.

Steps to reproduce

$ExecutionContext.SessionState.InvokeCommand.InvokeScript('"`$args:($args); `$input:($input)"', 1, 2, 3)

Expected behavior

$args:(1 2 3); $input:()

Actual behavior

$args:(); $input:(1 2 3)

Environment data

Tested in v2.0 and v5.1.15063.608