Edit

I've rewritten the loader to duplicate data if only one element (v, vt, vn) is different. I get a much better result, but it is still incorrect. The seams on the mesh match what they should look like, but the texture appears a bit deformed. I've checked a list of the texture coords, and there appear to be some missing, but I don't understand how this could happen.

Here is the new code:

int bytesLoaded = 0;
    
    ArrayList<Float> vertices = new ArrayList<>();
    ArrayList<Float> textureCoords = new ArrayList<>();
    ArrayList<Float> normals = new ArrayList<>();
    
    ArrayList<Float> plainVertices = new ArrayList<>();
    ArrayList<Float> plainTextureCoords = new ArrayList<>();
    ArrayList<Float> plainNormals = new ArrayList<>();
    
    ArrayList<Integer> indices = new ArrayList<>();
    ArrayList<String> writtenData = new ArrayList<>();
    
    String line;
    
    try {
        InputStream stream = IO.class.getClassLoader().getResourceAsStream(filePath); //get file off classpath
        BufferedReader reader = new BufferedReader(new InputStreamReader(stream)); //create file reader
        
        while((line = reader.readLine())!=null) { //repeat until document's end has been reached
            String[] data = line.split(" "); //split line into each data point
            
            if (line.startsWith("v ")) { //add vertices in the 3 data points, excluding the first which is the "v"
                for (int i=1; i<4; i++) {
                    plainVertices.add(Float.parseFloat(data[i]));
                }
                
            } else if (line.startsWith("vt ")) {
                for (int i=1; i<3; i++) {
                    plainTextureCoords.add(Float.parseFloat(data[i])); //add vertex textures in the 2 data points, excluding the first which is the "vt"
                }
                
            } else if (line.startsWith("vn ")) {
                for (int i=1; i<4; i++) {
                    plainNormals.add(Float.parseFloat(data[i])); //add vertices in the 3 data points, excluding the first which is the "vn"
                }
                
            } else if (line.startsWith("f ")) { //indices
                for (int i = 1; i<4; i++) {
                    String[] faceIndices = data[i].split("/"); //split each face into v indice, vt indice and vn indice
                    
                    int vertexIndex = Integer.parseInt(faceIndices[0]) - 1; //get the indices, subtract 1 because OpenGL indices are 0 indexed
                    int textureCoordIndex = Integer.parseInt(faceIndices[1]) - 1;
                    int normalIndex = Integer.parseInt(faceIndices[2]) - 1;
                    
                    StringBuilder tokenBuilder = new StringBuilder(); //generate a unique token to prevent repeats
                    tokenBuilder.append(vertexIndex);
                    tokenBuilder.append("+");
                    tokenBuilder.append(textureCoordIndex);
                    tokenBuilder.append("+");
                    tokenBuilder.append(normalIndex);

                    String token = tokenBuilder.toString(); 
                    System.out.println(token);
                    
                    if (!writtenData.contains(token)) { //add the 3 indices' values to their list
                        writtenData.add(token);
                        
                        vertices.add(plainVertices.get(vertexIndex * 3));
                        vertices.add(plainVertices.get(vertexIndex * 3 + 1));
                        vertices.add(plainVertices.get(vertexIndex * 3 + 2));
                        
                        textureCoords.add(plainTextureCoords.get(textureCoordIndex * 2));
                        textureCoords.add(plainTextureCoords.get(textureCoordIndex * 2 + 1));
                        
                        normals.add(plainNormals.get(normalIndex * 3));
                        normals.add(plainNormals.get(normalIndex * 3 + 1));
                        normals.add(plainNormals.get(normalIndex * 3 + 2));
                    
                    }
                    
                    indices.add(writtenData.indexOf(token)); //generate an index
                }
            }
            bytesLoaded = bytesLoaded + line.getBytes().length; //keep track of bytes loaded
            //System.out.println(bytesLoaded);
        }

Original