Why does this happen?
The term "building" is an abstraction in Eclipse denoting the process of transforming the available resources in the workspace into some result. Any plugin can contribute builders for processing the workspace's resources. Some of the builders are truly compilers that transform the source code into a binary form. But most of the builders in Eclipse are actually validators that just check the source code for problems and add error and warning markers.
Eclipse started as a Java IDE. The primary reason for introducing the builders in the Eclipse Platform was to compile the Java source code into bytecode that can be executed by the JVM. It was important to ensure that the building process has finished before launching the Java program. Otherwise the launched program may be broken because some classes are still being compiled. Therefore, the launching infrastructure was implemented to block if any builders are still running and to wait for their execution to finish.
While the above makes sense for Java, it does not for many other programming languages that Eclipse supports today. The builders that run for a PHP project, for example, are just to validate the code and are not a prerequisite for its successful execution.
What is the solution?
Fortunately, the behavior of the program launching infrastructure can be configured. There is a preference that determines if the program launch should wait for the build to finish.
The preference is on the "Run/Debug > Launching" preference page. Look for the group of radio buttons with title "Wait for ongoing build to complete before launching". Usually the default value "Always" is selected, which follows the behavior described so far. Selecting "Never" will switch the waiting for the build off, while "Prompt" will display a dialog asking whether to wait for the build or not. The latter option is useful if your workspace contains programs written in both compiled and interpreted languages.