Time – and the major events we use to define it – has flexed with our increasing ability to measure it. Thus, our years aren’t exactly 365 days long. The Earth takes a little longer than that to get around the Sun, so we occassionally have leap years.
Similarly, since the length of a day – 24 hours of 60 minutes of 60 seconds – was defined, scientists have been able to make increasingly accurate measurements of the time it takes the earth to turn on its axis. And from time to time – 23 times, in fact, since 1972 – scientists have had to add leap seconds.
2009 thus started one second later than you would normally have expected it to. This BBC article gives more detail on why and how. It also describes how the keepers of Big Ben adjust its running time by inserting pennies into the works to slow things down.