Output from amplifier is clipping
You might need to look for rail to Rail op-amps if the output of op-amp is expected to be close to supply voltage.
Below spec is from datasheet of LM358 op-amp which tells that the difference can be upto 1.5 V from the VCC (3 V, in OP case)



Suggestion: 

MCP6001 from Microchip. Datasheet here