You don't (necessarily) need to get rid of warnings. A warning is ok if you agree or accept it, it is an error if you disagree with it.

In the case you mention above, you have 4 pipes framing into the same node. From an "SIF point of view", the Codes don't address this configuration. This is why CAESAR II displays the warning.

So, if you've attempted to model a "cross" here, CAESAR II will not compute SIFs for you, and you need to do further research. On the other hand, if this node is a node with 2 pipes and 2 dummy elements, then everything is ok. Additionally, if at this node you expected only 3 pipes and CAESAR II is reporting 4, then you have a geometry error that you should correct.

CAESAR II doesn't know what is going on, you have to decide what is acceptable.