Classes compile outside vscode in CLI, but in vs-code problem section displays errors and editor highlights code lines in red

Java Code is compiling neatly, outside the Vs-Code IDE i.e., from command line and other IDE's like IntelliJ, but when I import my project into VS-Code there are some errors displayed in problems section. Some of them are shown here with screenshots

Environment

• Operating System: Windows 10
• JDK version: 1.8 - J9 VM
• Visual Studio Code version: 1.47.2
• Java extension version: v0.64
• Build tool: Gradle, wrapper version, 4.8.1

Steps To Reproduce the

1. Create a project having src/main/resources and add your java code directly inside src\main
2. Java Model Exception: Java Model Status [Cannot nest '<project>/src/main/resources' inside '<project>/src/main'. To enable the nesting exclude 'resources/' from 'junit_tests/src/main']

Current Result

• Below is the Java language server log file excerpt
  

• I have tried excluding the resources folder, but no luck, problems section still has this.

• All these compile times issues or problems shown in the problems section in vsc-code are not detected in IntelliJ IDE. Not sure why the is is happening.

• The code/java intellisense cannot trace the relationship between so, red marks with lines highlighted is shown, but actually that's not the case, as the classes are compiled perfectly from command line.

• Some of the compiler issues, shown in the problems section are
  -

•