Actually it is not a bug.
DBeaver has two modes of SQL execution: statement (CTRL+Enter) and script (ALT+X).
In statement mode it extracts current statement (it is statement where cursor is positioned and it is delimited by empty lines or by ";" symbol). It allows you to have many SQL statements in a single SQL editor and execute any of them at any time. It is very convinient if many cases. Empty line as statement delimiter is very native and visual way to structurize text.
Also you may select any part of SQL text and press CTRL+Enter - dbeaver will execute only selected text.
In script mode dbeaver executes entire SQL script. It will split script on statements using ";" symbol (empty lines have no meaning in this mode) and then execute them one by one.
So, if you want to execute single statement which contains empty line you have to select this statement and press CTRL+Enter.
Probably we can somehow improve SQL execution. But at the moment I don't have any good ideas about it.