The massacre of the SS guards at Dachau is one particular example of allied war crimes in germany.

The liberation of Dachau concentration camp by the US army was preceded by days of constant revelations of nazi atrocities including finding thousands of putrefying, emaciated bodies in train cars, some with evidence of extreme physical trauma (brain matter from a head wound left to rot) lying where they died in their own excrement. You can imagine then that the US soldiers were not feeling particularly sympathetic to the SS and prisoner-guards (Kapo) they captured.

Reports vary on what happened from then on. One testimony by Lt. Colonel Felix Sparks stated that after leaving 50 or so SS guards in a coal store under the watch of an unnamed machinegunner referred to as "birdeye". It is claimed that as soon as Sparks left he heard birdeye yell that the prisoners were trying to escape followed by a burst of machinegun fire killing 12 guards. Birdeye was found to be crying hysterically at this point and was relieved of his duties. According to sparks the number of dead germans did not exceed more than 30.

This however is refuted by another witness, First Lietenant Howard Beuchner alleged that after the first shooting further SS guards were lined up against a wall and shot. Buechener testified that over the course of the day up to 520 germans were killed in reprisals, however this is disputed by some as being baseless.

A recently unearthed testamant by US army medic Captain David Wilsey has backed up the claim that 15/16 guards were lined up and shot against a wall by US servicemen. Wilsey said he watched "without emotion" as the guards "so had it coming". He also claims that guards were made to stand naked in heil Hitler stances for hours while cold water was poured on them. Wilsey also admitted to looting items from the camp which he sent back to his wife, it is unclear whether these were looted from germans or prisoners.

(http://www.dailymail.co.uk/news/article-3088025/How-American-doctor-witnessed-Dachau-s-SS-guards-tortured-shot-dead-GIs-cold-blood-coming.html) (sorry for daily fail link)

Further allegations include the distribution of weapons to some surviving prisoners who then "tore apart" Kapo members. Also it is alleged that US soldiers turned a blind eye to prisoners beating guards to death with shovels and their hands.

The reason you may not have herd of these events include the obvious lack of sympathy for those killed, and that General Patton decided not to prosecute those involved.

Other more well known war crimes are the frequently denied (but definitely happened) mass raping of civilians in Soviet occupied territories that I'm sure someone else will be able to explain more thoroughly.