The issue is JAVA Bindings for BAseX version <= 7.7, illustrated by the following XQUERY code

import module namespace set = "java.util.HashSet";{

let $loop :=
for $i in 1 to 128
return set:add($i)

let $loop :=
for $i in 1 to 128
return set:add($i)
return
set:size()
}

returning .. 129 (expected 128)

Explanation : (courtesy by Christian Gruen)

• The set:add function is no integer-specific function, so it allows all types of objects as argument.
• This is why the XQuery item will not be explicitly cast to an integer; instead, the original Java XQuery Item object will be passed on to the Java function.
• In BaseX, the first items of type xs:integer and in the range of 0-127 are cached. This means that if an integer like 84 is requested twice, the returned item will have the same reference in memory.
• This is different for integers larger than 127: in this case, new references will be created. As XQuery items have nohashCode() function, their memory reference will be used when calculating the hash code.

WorkAround : 

preferred : Last Stable Release 7.8 solves the issue.

Other  workaround : 

- Use the map:module to simulate HashSet (well, I do confess that I do not know how to achieve this)

- wrap the JAVA Class in order to manage directly this issue (by forcing cast operation in your wrapper), then import your wrapper as a module in BAseX