Joining arrays of vectors of abritrary lengths

General Usage
2

Your error is here:

julia> merged_stack = Array{Any}(undef, 3, 3)
3×3 Matrix{Any}:
 #undef  #undef  #undef
 #undef  #undef  #undef
 #undef  #undef  #undef

julia> fill!(merged_stack, Float64[])
3×3 Matrix{Any}:
 Float64[]  Float64[]  Float64[]
 Float64[]  Float64[]  Float64[]
 Float64[]  Float64[]  Float64[]

julia> append!(merged_stack[1,1],[1.0,2.0])
2-element Vector{Float64}:
 1.0
 2.0

julia> merged_stack
3×3 Matrix{Any}:
 [1.0, 2.0]  [1.0, 2.0]  [1.0, 2.0]
 [1.0, 2.0]  [1.0, 2.0]  [1.0, 2.0]
 [1.0, 2.0]  [1.0, 2.0]  [1.0, 2.0]

The fill! fills merged_stack with the same object. Alle the empty arrays Float64[] are a single object.
There are several ways to achieve what you need, typically, I don’t have the most efficient way, but others will provide them.
You can do with a loop for example:

julia> merged_stack = Array{Vector{Float64}}(undef, 3, 3)
3×3 Matrix{Vector{Float64}}:
 #undef  #undef  #undef
 #undef  #undef  #undef
 #undef  #undef  #undef

julia> for index in eachindex(merged_stack)
           merged_stack[index]=Float64[]
       end

julia> append!(merged_stack[1,1],[1.0,2.0])
2-element Vector{Float64}:
 1.0
 2.0

julia> merged_stack
3×3 Matrix{Any}:
 [1.0, 2.0]  Float64[]  Float64[]
 Float64[]   Float64[]  Float64[]
 Float64[]   Float64[]  Float64[]
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