Spot metering isolates a small area of the scene - usually a small circular area in the centre - from which to meter, which means the metering is not affected by tones around the edges of the scene. If you were spot metering from the bird then the exposure should have brightened up, unless the bird was too small to be of significance in the frame.
In your case you were setting the exposure manually, which means it's down to you to decide what the exposure should look like. If all you did was to aim randonly into the scene and to adjust settings until the meter needle was centred then I'm afraid you need a better understanding of how to meter and set exposure.
If you look at the shot you've just posted above then you could use the spot meter to meter just from the white door, or just from the bird table, or anything else you were specifically interested in. Whatever thing you choose, when the meter needle is centred it will try to record that object as a "middle tone". Your white door would come out too dark. Your dark bird table would come out too bright. You need to figure out how bright those things should appear in the photograph and adjust the camera setting so that white looks white rather than grey, and so on. The white door should be at perhaps +2. The bird table at around -1, the bricks at around +0. Experience will allow your estimations to become more accurate.
Dust bunnies are dust on the sensor. Dust on the lens is unlikely to show up in your photographs.