In China, Japan's war was not formally for liberation (China was not a colony), but was simply to punish the Chinese. Japan believed that they were the sole Great Power in the region and that they had the right to defend their interests in Manchuria. Younger officers, whose image of China was highly colored by racism, felt sure that China could not hold out long against Japanese attack, and that their hubris at the Manchurian border deserved punishment. In fact the Chinese Republican army was steadily gaining in power, and from the Chinese perspective Manchuria was being occupied and Japan had no right to be there. The 1937 war was explicitly punitive in nature and Chinese rebels had already been considered subhuman for half a decade, so it's not surprising that although big hearted theorists of the "co-prosperity sphere" called for gentle treatment, the Japanese soldiers were given free reign on the ground.
In Southeast Asia, Japan had a problem familiar to all unwelcome occupiers of that region. While the philosophical plan was for liberation, in practice they were not bringing anything with them but force, and natives knew the difficult terrain much better than them. Japan needed to extract resources from occupied regions and needed to subdue resistance at any cost. The amount of sheer massacre committed in the name of liberation has parallels to the Indonesian occupation of East Timor and the American occupation of the Philippines.
As described in the comments underneath the question, the Japanese army was unprepared for a liberation war in many ways, including a culture of corporal punishment within the army that would be considered brutal and criminal today. There were official attempts at propagandizing which had some effect on intellectuals, but ordinary peasants on the ground were much more viscerally affected by Japanese tendency towards brutality.
