We present pulse timing analysis of Rossi X-ray Timing Explorer ( RXTE ) observations of the anomalous X-ray pulsar 1E 2259+586 from its 2002 outburst to October 2010 . Our objectives are to extend the work on the recovery stage after the 2002 glitch , investigate the variations caused by the second glitch which occurred in 2007 and look for other unusual events , if any , that arise in the regular spin-down trend of the source . We find that the fractional change in the spin frequency derivative after the 2002 glitch is not stable since it decreased an order of magnitude , from -2.2 \times 10 ^ { -2 } to -1.278 ( 3 ) \times 10 ^ { -3 } , in about 2.5 years . From pulse timing analysis , we discover two small frequency shifts with fractional changes \Delta \nu / \nu = 3.08 ( 32 ) \times 10 ^ { -8 } and \Delta \nu / \nu = -1.39 ( 11 ) \times 10 ^ { -8 } . While the first one of these shifts is not found to have a fractional frequency derivative change while second one has \Delta \dot { \nu } / \dot { \nu } = -2.9 ( 2 ) \times 10 ^ { -2 } . We interpret these frequency changes as positive and negative microglitches similar to those seen in radio pulsars .