It is simply as that : when you put 2 pipes and you want to connect them with pipe wire, you need to put 1 extra pipe wire at the intersection between the 2 pipes.

Here's the setup :

I put one pipe and a pipe wire segment on it :

I put another pipe next to it with a pipe wire on it as well :

You can see that there's a gap between the 2 pipe wires ! However if I place a Gate on the pipe, everything become normal :

BuildCraft version : 7.2.5
Extra mods : Optifine