The presence of redstone lamps, droppers, dispensers, and command blocks in a device can change the behavior of observers and possibly other redstone components in the same device, despite that they should not be affecting them in any way.

Screenshots and a world download are attached.

The test world contains two identical test jigs. The first jig works as expected; the second one does not. Each time you build this jig in another location, there is a random chance that it will work as expected. Once built, a jig's behavior does not change; one that exhibits the problem always exhibits it in the same way, while one that doesn't exhibit the problem never exhibits it.

The test jig is designed to produce a sequence of 1-tick pulses out of the sideways facing observers, 1 tick apart, in order from bottom to top. It has a memory display at the top (on the green blocks) that records the pattern of output pulses from the top sideways facing observer. At the bottom of the jig is a red block on which a test component can be placed.

Expected behavior: The topmost sideways facing observer emits a 1-rtick pulse, regardless of what, if anything, is on the red block.

Actual behavior (in a jig that exhibits the problem): The output varies depending on which, if any, component is on the red block, and in the case of the command block, what its settings are set to.

Steps to reproduce: (repeat on each jig):
1. Ensure that the memory display is clear (break/replace the dust on the blue block).
2. Place a redstone lamp, dropper, dispenser, or command block on the red block, facing in any direction other than the observer. (See note below for command block settings). Alternatively, remove any component to test without one.
3. Toggle the lever.
4. Examine the memory display. Note that jig 1 always displays a single on-pulse, while jig 2 displays one of the following sequences of pulses:

5. As a test variation, break some combination of the 2nd through 5th sideways facing observers, counting from the bottom, and repeat the test. Note that the displayed pulse pattern may change. (I think that if you break both the 2nd and 3rd observers from the bottom, the problem disappears.) If no component is on the red block, breaking these observers has no effect on the output.

Note: The command block behavior depends on its settings. Not all settings cause unexpected output. Known settings which do include (Impulse, Unconditional, Needs Redstone) and (Repeat, Unconditional, Needs Redstone). It is not necessary to enter a command into the block.