Without knowing which plans you are asking about, it is hard to answer this question accurately.  However, we can say that there were at least three reasons why Congress sometimes blocked Kennedy's plans.  They include:

• He lacked a mandate.  Kennedy won the 1960 election by the slimmest of margins.  This showed that he did not have overwhelming public support behind him and gave Congress the feeling they could oppose him without fear.
• Congress was not very liberal.  The split in Congress between Republicans and Democrats was pretty narrow.  In addition, many Democrats were Southerners who were really quite conservative.  This meant there was a lot of resistance to Kennedy's more liberal proposals.
• Kennedy was not very skilled in working with Congress.  Kennedy was not like Lyndon Johnson who really knew how to "work" Congress.  This meant that he was not as good at persuading members of Congress to agree with him.