There are at least four possible causes for this issue.


Firstly, let's dissect the syntax of the /fill command, though, with focus on the replace feature.

/fill x1 y1 z1 x2 y2 z2 block_type_1 replace block_type_2

/fill - the command. This tells the game what feature it should execute.

x1, y1, z1 - the coordinates of the first corner. This tells the game where it should start filling.
x2, y2, z2 - the coordinates of the second corner. This tells the game where it should stop filling.
It will fill every block with the coordinates of any x between x1 and x2, any y between y1 and y2 and any z between z1 and z2.

block_type_1 - this tells the game what block you want to fill this are with. This is the block that will be placed on the fitting coordinates after passing through the additional, optional arguments.

replace - the additional optional argument. This tells the game that it should only replace blocks of a certain type. This argument has no effect without including the next one.

block_type_2 - this tells the game what block type you want to be replaced. This is the block that will be replaced by block_type_1 if it has fitting coordinates.


Now, let's take your command as an example and say what it does by running it through the list I've compiled.

/fill ~50 ~1 ~50 ~-50 ~-1 ~-50 minecraft:grass_block replace minecraft:jungle_wood

x1 = ~50
y1 = ~1
z1 = ~50

x2 = ~-50
y2 = ~-1
z2 = ~-50

block_type_1 = minecraft:grass_block
block_type_2 = minecraft:jungle_wood

This tells the game that it should fill all blocks that are within 50 blocks on each horizontal axis and 1 block on the vertical of the player, with blocks of type minecraft:grass_block, but only if the block was of type minecraft:jungle_wood before this command was executed.

In short, it means it replaces all jungle wood within the cuboid with grass blocks.


Now that we know exactly what the command does when executed, the next step is to troubleshoot.

Here are the possible reasons why the command doesn't work as expected.

1. There might be no blocks of this type in that area

Check if there really is jungle wood within the cuboid to be replaced with grass blocks. Try:

1. Checking your command. Are you sure you want to replace jungle wood with grass blocks, and not the other way around?

2. Using the testforblocks command to see if there are blocks of that type in the area.
   
   
   

2. The command might be used by a plugin, preventing it from working

If you are playing on a multiplayer server with plugins installed, one of the plugins might include a /fill command that functions similarly to the Minecraft version, however produces a different result.

If this is the case, try executing the command with the prefix minecraft: instead. (/minecraft:fill ...)

3. Your installation of Minecraft might be corrupted

Despite this being extremely unlikely, if no other solutions work, it is worth trying to reinstall Minecraft, as during the installation, an error might have occured.

4. Your installation of Java might be outdated or corrupted

This option is still highly unlikely, however if the problem persists, try updating or reinstalling Java on your device. Stay away from development/unstable builds as they might have some mistakes/typos in them.

Only download Java from the official website.