The failure of an individual LED to light may or may not indicate a faulty circuit on the MDL645 module. Since you said you touched +24v to the individual terminals, I'm going to assume you have the negative side of the DC supply connected to terminal 1. That makes it a sinking input which must be connected to a sourcing device. The +24v supply qualifies as a sourcing device.
If there are no connections to any of the I1 - I16 terminals, then touching +24v to them should light the LED. If it fails to light, then that input point is probably bad. The LEDs are on the field wiring side of the module, so failure to light means no current flow.
If there are field devices connected to the I1 - I16 terminals, it gets a little more complicated. It's possible that the +24v can backfeed to ground through the field device. If the 24 volt supply can't handle the current draw its voltage will drop and you won't see the LED light up. On the circuits that don't light the LEDs, check the +24v level with a meter while you touch it to the terminal. If you can maintain +24v then you can draw the same conclusion as when you touch +24v to an unconnected terminal. Either that or disconnect the field wire when you touch the +24v to the terminal.
You should also check the integrity of the connection at terminal 1. If the negative side of the DC supply is not actually connected to it, then you might possibly see some LEDs light and others not. It's also possible that in touching +24 to some of the input terminals you move the wire to terminal 1 and disconnect it.
