A single stage common emitter amplifier WILL invert the signal.
The output of the 555 goes high for a short duration, putting current into the base of the transistor. This causes the transistor to conduct from collector to emitter, causing a current to flow in the collector resistor.
When there is no collector current, there will be no volt drop across the collector resistor and so the voltage at the collector will be the same as the supply voltage.
When collector current flows, there will be volt drop across the collector resisitor and the voltage at the collector will be reduced, ie, supply voltage - voltdrop in collector resistor.
So what you are seeing is quite normal.
If you want to have a short duration +ve going pulse, an obvious way to fix it would be to just have a short duration -ve going pulse out of the 555.
In other words, the opposite of what you have now.
JimB